diff --git a/mypy/errors.py b/mypy/errors.py
index 4e62a48aeb27..427659253540 100644
--- a/mypy/errors.py
+++ b/mypy/errors.py
@@ -503,6 +503,9 @@ def add_error_info(self, info: ErrorInfo) -> None:
                         self.used_ignored_lines[file][scope_line].append(
                             (info.code or codes.MISC).code
                         )
+                        if file not in self.ignored_files:
+                            info.hidden = True
+                            self._add_error_info(file, info)
                         return
             if file in self.ignored_files:
                 return
@@ -724,6 +727,8 @@ def generate_unused_ignore_errors(self, file: str) -> None:
                 blocker=False,
                 only_once=False,
                 allow_dups=False,
+                origin=(self.file, [line]),
+                target=self.target_module,
             )
             self._add_error_info(file, info)
 
@@ -776,6 +781,8 @@ def generate_ignore_without_code_errors(
                 blocker=False,
                 only_once=False,
                 allow_dups=False,
+                origin=(self.file, [line]),
+                target=self.target_module,
             )
             self._add_error_info(file, info)
 
@@ -800,8 +807,9 @@ def blocker_module(self) -> str | None:
         return None
 
     def is_errors_for_file(self, file: str) -> bool:
-        """Are there any errors for the given file?"""
-        return file in self.error_info_map
+        """Are there any visible errors for the given file?"""
+        errors = self.error_info_map.get(file, ())
+        return any(error.hidden is False for error in errors)
 
     def prefer_simple_messages(self) -> bool:
         """Should we generate simple/fast error messages?
diff --git a/mypy/server/update.py b/mypy/server/update.py
index 0cc7a2229514..0371d5d40266 100644
--- a/mypy/server/update.py
+++ b/mypy/server/update.py
@@ -667,6 +667,8 @@ def restore(ids: list[str]) -> None:
     state.type_check_first_pass()
     state.type_check_second_pass()
     state.detect_possibly_undefined_vars()
+    state.generate_unused_ignore_notes()
+    state.generate_ignore_without_code_notes()
     t2 = time.time()
     state.finish_passes()
     t3 = time.time()
@@ -1028,6 +1030,10 @@ def key(node: FineGrainedDeferredNode) -> int:
         if graph[module_id].type_checker().check_second_pass():
             more = True
 
+    graph[module_id].detect_possibly_undefined_vars()
+    graph[module_id].generate_unused_ignore_notes()
+    graph[module_id].generate_ignore_without_code_notes()
+
     if manager.options.export_types:
         manager.all_types.update(graph[module_id].type_map())
 
diff --git a/test-data/unit/daemon.test b/test-data/unit/daemon.test
index 18a03a92207d..d772635ac027 100644
--- a/test-data/unit/daemon.test
+++ b/test-data/unit/daemon.test
@@ -571,3 +571,113 @@ class A:
     x: int
 class B:
     x: int
+
+[case testUnusedTypeIgnorePreservedOnRerun]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --warn-unused-ignores --no-error-summary --hide-error-codes
+Daemon started
+$ dmypy check -- bar.py
+bar.py:2: error: Unused "type: ignore" comment
+== Return code: 1
+$ dmypy check -- bar.py
+bar.py:2: error: Unused "type: ignore" comment
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+a = 1  # type: ignore
+
+[case testTypeIgnoreWithoutCodePreservedOnRerun]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --enable-error-code ignore-without-code --no-error-summary
+Daemon started
+$ dmypy check -- bar.py
+bar.py:2: error: "type: ignore" comment without error code  [ignore-without-code]
+== Return code: 1
+$ dmypy check -- bar.py
+bar.py:2: error: "type: ignore" comment without error code  [ignore-without-code]
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+a = 1  # type: ignore
+
+[case testUnusedTypeIgnorePreservedAfterChange]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --warn-unused-ignores --no-error-summary --hide-error-codes
+Daemon started
+$ dmypy check -- bar.py
+bar.py:2: error: Unused "type: ignore" comment
+== Return code: 1
+$ echo '' >> bar.py
+$ dmypy check -- bar.py
+bar.py:2: error: Unused "type: ignore" comment
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+a = 1  # type: ignore
+
+[case testTypeIgnoreWithoutCodePreservedAfterChange]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --enable-error-code ignore-without-code --no-error-summary
+Daemon started
+$ dmypy check -- bar.py
+bar.py:2: error: "type: ignore" comment without error code  [ignore-without-code]
+== Return code: 1
+$ echo '' >> bar.py
+$ dmypy check -- bar.py
+bar.py:2: error: "type: ignore" comment without error code  [ignore-without-code]
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+a = 1  # type: ignore
+
+[case testPossiblyUndefinedVarsPreservedAfterUpdate]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --enable-error-code possibly-undefined --no-error-summary
+Daemon started
+$ dmypy check -- bar.py
+bar.py:4: error: Name "a" may be undefined  [possibly-undefined]
+== Return code: 1
+$ dmypy check -- bar.py
+bar.py:4: error: Name "a" may be undefined  [possibly-undefined]
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+if False:
+    a = 1
+a
+
+[case testReturnTypeIgnoreAfterUnknownImport]
+-- Return type ignores after unknown imports and unused modules are respected on the second pass.
+$ dmypy start -- --warn-unused-ignores --no-error-summary
+Daemon started
+$ dmypy check -- foo.py
+foo.py:2: error: Cannot find implementation or library stub for module named "a_module_which_does_not_exist"  [import-not-found]
+foo.py:2: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+== Return code: 1
+$ dmypy check -- foo.py
+foo.py:2: error: Cannot find implementation or library stub for module named "a_module_which_does_not_exist"  [import-not-found]
+foo.py:2: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+== Return code: 1
+
+[file unused/__init__.py]
+[file unused/empty.py]
+[file foo.py]
+from unused.empty import *
+import a_module_which_does_not_exist
+def is_foo() -> str:
+    return True  # type: ignore
diff --git a/test-data/unit/fine-grained.test b/test-data/unit/fine-grained.test
index 68f72a2aa992..6cae8a81bf51 100644
--- a/test-data/unit/fine-grained.test
+++ b/test-data/unit/fine-grained.test
@@ -5390,6 +5390,7 @@ from enum import Enum
 
 class C(Enum):
     X = 0
+[builtins fixtures/tuple.pyi]
 [typing fixtures/typing-medium.pyi]
 [out]
 ==
@@ -5486,6 +5487,7 @@ C = Enum('C', 'X Y')
 from enum import Enum
 
 C = Enum('C', 'X')
+[builtins fixtures/tuple.pyi]
 [typing fixtures/typing-medium.pyi]
 [out]
 ==
diff --git a/test-data/unit/fixtures/async_await.pyi b/test-data/unit/fixtures/async_await.pyi
index 96ade881111b..28daa0321947 100644
--- a/test-data/unit/fixtures/async_await.pyi
+++ b/test-data/unit/fixtures/async_await.pyi
@@ -1,9 +1,12 @@
 import typing
+from typing_extensions import override
 
 T = typing.TypeVar('T')
 U = typing.TypeVar('U')
 class list(typing.Sequence[T]):
+    @override
     def __iter__(self) -> typing.Iterator[T]: ...
+    @override
     def __getitem__(self, i: int) -> T: ...
     def __contains__(self, item: object) -> bool: ...
 
diff --git a/test-data/unit/fixtures/dataclasses.pyi b/test-data/unit/fixtures/dataclasses.pyi
index 059c853a621f..29f87ae97e62 100644
--- a/test-data/unit/fixtures/dataclasses.pyi
+++ b/test-data/unit/fixtures/dataclasses.pyi
@@ -3,6 +3,7 @@ from typing import (
     Generic, Iterator, Iterable, Mapping, Optional, Sequence, Tuple,
     TypeVar, Union, overload,
 )
+from typing_extensions import override
 
 _T = TypeVar('_T')
 _U = TypeVar('_U')
@@ -29,8 +30,10 @@ class dict(Mapping[KT, VT]):
     def __init__(self, **kwargs: VT) -> None: pass
     @overload
     def __init__(self, arg: Iterable[Tuple[KT, VT]], **kwargs: VT) -> None: pass
+    @override
     def __getitem__(self, key: KT) -> VT: pass
     def __setitem__(self, k: KT, v: VT) -> None: pass
+    @override
     def __iter__(self) -> Iterator[KT]: pass
     def __contains__(self, item: object) -> int: pass
     def update(self, a: Mapping[KT, VT]) -> None: pass
@@ -42,7 +45,9 @@ class dict(Mapping[KT, VT]):
 
 class list(Generic[_T], Sequence[_T]):
     def __contains__(self, item: object) -> int: pass
+    @override
     def __getitem__(self, key: int) -> _T: pass
+    @override
     def __iter__(self) -> Iterator[_T]: pass
 
 class function: pass
diff --git a/test-data/unit/fixtures/dict.pyi b/test-data/unit/fixtures/dict.pyi
index 19d175ff79ab..dfb7fab13422 100644
--- a/test-data/unit/fixtures/dict.pyi
+++ b/test-data/unit/fixtures/dict.pyi
@@ -5,6 +5,7 @@ import _typeshed
 from typing import (
     TypeVar, Generic, Iterable, Iterator, Mapping, Tuple, overload, Optional, Union, Sequence
 )
+from typing_extensions import override
 
 T = TypeVar('T')
 KT = TypeVar('KT')
@@ -23,8 +24,10 @@ class dict(Mapping[KT, VT]):
     def __init__(self, **kwargs: VT) -> None: pass
     @overload
     def __init__(self, arg: Iterable[Tuple[KT, VT]], **kwargs: VT) -> None: pass
+    @override
     def __getitem__(self, key: KT) -> VT: pass
     def __setitem__(self, k: KT, v: VT) -> None: pass
+    @override
     def __iter__(self) -> Iterator[KT]: pass
     def __contains__(self, item: object) -> int: pass
     def update(self, a: SupportsKeysAndGetItem[KT, VT]) -> None: pass
@@ -46,7 +49,9 @@ class str: pass # for keyword argument key type
 class bytes: pass
 
 class list(Sequence[T]): # needed by some test cases
+    @override
     def __getitem__(self, x: int) -> T: pass
+    @override
     def __iter__(self) -> Iterator[T]: pass
     def __mul__(self, x: int) -> list[T]: pass
     def __contains__(self, item: object) -> bool: pass
diff --git a/test-data/unit/fixtures/list.pyi b/test-data/unit/fixtures/list.pyi
index 90fbabe8bc92..ac5b7e49b147 100644
--- a/test-data/unit/fixtures/list.pyi
+++ b/test-data/unit/fixtures/list.pyi
@@ -1,6 +1,7 @@
 # Builtins stub used in list-related test cases.
 
 from typing import TypeVar, Generic, Iterable, Iterator, Sequence, overload
+from typing_extensions import override
 
 T = TypeVar('T')
 
@@ -15,11 +16,13 @@ class list(Sequence[T]):
     def __init__(self) -> None: pass
     @overload
     def __init__(self, x: Iterable[T]) -> None: pass
+    @override
     def __iter__(self) -> Iterator[T]: pass
     def __len__(self) -> int: pass
     def __contains__(self, item: object) -> bool: pass
     def __add__(self, x: list[T]) -> list[T]: pass
     def __mul__(self, x: int) -> list[T]: pass
+    @override
     def __getitem__(self, x: int) -> T: pass
     def __setitem__(self, x: int, v: T) -> None: pass
     def append(self, x: T) -> None: pass
diff --git a/test-data/unit/fixtures/plugin_attrs.pyi b/test-data/unit/fixtures/plugin_attrs.pyi
index 57e5ecd1b2bc..ffaa82798ae7 100644
--- a/test-data/unit/fixtures/plugin_attrs.pyi
+++ b/test-data/unit/fixtures/plugin_attrs.pyi
@@ -1,5 +1,6 @@
 # Builtins stub used to support attrs plugin tests.
 from typing import Union, overload, Generic, Sequence, TypeVar, Type, Iterable, Iterator
+from typing_extensions import override
 
 class object:
     def __init__(self) -> None: pass
@@ -31,6 +32,8 @@ T = TypeVar("T")
 Tco = TypeVar('Tco', covariant=True)
 class tuple(Sequence[Tco], Generic[Tco]):
     def __new__(cls: Type[T], iterable: Iterable[Tco] = ...) -> T: ...
+    @override
     def __iter__(self) -> Iterator[Tco]: pass
     def __contains__(self, item: object) -> bool: pass
+    @override
     def __getitem__(self, x: int) -> Tco: pass
diff --git a/test-data/unit/fixtures/primitives.pyi b/test-data/unit/fixtures/primitives.pyi
index 63128a8ae03d..bc75aa70b6ed 100644
--- a/test-data/unit/fixtures/primitives.pyi
+++ b/test-data/unit/fixtures/primitives.pyi
@@ -1,6 +1,7 @@
 # builtins stub with non-generic primitive types
 import _typeshed
 from typing import Generic, TypeVar, Sequence, Iterator, Mapping, Iterable, Tuple, Union
+from typing_extensions import override
 
 T = TypeVar('T')
 V = TypeVar('V')
@@ -27,35 +28,48 @@ class complex:
 class bool(int): pass
 class str(Sequence[str]):
     def __add__(self, s: str) -> str: pass
+    @override
     def __iter__(self) -> Iterator[str]: pass
     def __contains__(self, other: object) -> bool: pass
+    @override
     def __getitem__(self, item: int) -> str: pass
     def format(self, *args: object, **kwargs: object) -> str: pass
 class bytes(Sequence[int]):
+    @override
     def __iter__(self) -> Iterator[int]: pass
     def __contains__(self, other: object) -> bool: pass
+    @override
     def __getitem__(self, item: int) -> int: pass
 class bytearray(Sequence[int]):
     def __init__(self, x: bytes) -> None: pass
+    @override
     def __iter__(self) -> Iterator[int]: pass
     def __contains__(self, other: object) -> bool: pass
+    @override
     def __getitem__(self, item: int) -> int: pass
 class memoryview(Sequence[int]):
     def __init__(self, x: bytes) -> None: pass
+    @override
     def __iter__(self) -> Iterator[int]: pass
     def __contains__(self, other: object) -> bool: pass
+    @override
     def __getitem__(self, item: int) -> int: pass
 class tuple(Generic[T]):
     def __contains__(self, other: object) -> bool: pass
 class list(Sequence[T]):
+    @override
     def __iter__(self) -> Iterator[T]: pass
     def __contains__(self, other: object) -> bool: pass
+    @override
     def __getitem__(self, item: int) -> T: pass
 class dict(Mapping[T, V]):
+    @override
     def __iter__(self) -> Iterator[T]: pass
 class set(Iterable[T]):
+    @override
     def __iter__(self) -> Iterator[T]: pass
 class frozenset(Iterable[T]):
+    @override
     def __iter__(self) -> Iterator[T]: pass
 class function: pass
 class ellipsis: pass
@@ -64,7 +78,9 @@ class range(Sequence[int]):
     def __init__(self, __x: int, __y: int = ..., __z: int = ...) -> None: pass
     def count(self, value: int) -> int: pass
     def index(self, value: int) -> int: pass
+    @override
     def __getitem__(self, i: int) -> int: pass
+    @override
     def __iter__(self) -> Iterator[int]: pass
     def __contains__(self, other: object) -> bool: pass
 
diff --git a/test-data/unit/fixtures/set.pyi b/test-data/unit/fixtures/set.pyi
index 71d3bd2eee18..cbf801f0551a 100644
--- a/test-data/unit/fixtures/set.pyi
+++ b/test-data/unit/fixtures/set.pyi
@@ -1,6 +1,7 @@
 # Builtins stub used in set-related test cases.
 
 from typing import TypeVar, Generic, Iterator, Iterable, Set
+from typing_extensions import override
 
 T = TypeVar('T')
 
@@ -19,6 +20,7 @@ class ellipsis: pass
 
 class set(Iterable[T], Generic[T]):
     def __init__(self, iterable: Iterable[T] = ...) -> None: ...
+    @override
     def __iter__(self) -> Iterator[T]: pass
     def __contains__(self, item: object) -> bool: pass
     def __ior__(self, x: Set[T]) -> None: pass
diff --git a/test-data/unit/fixtures/tuple.pyi b/test-data/unit/fixtures/tuple.pyi
index e270f3d79d3e..3202d46c841b 100644
--- a/test-data/unit/fixtures/tuple.pyi
+++ b/test-data/unit/fixtures/tuple.pyi
@@ -2,7 +2,7 @@
 
 import _typeshed
 from typing import Iterable, Iterator, TypeVar, Generic, Sequence, Optional, overload, Tuple, Type
-
+from typing_extensions import override
 T = TypeVar("T")
 Tco = TypeVar('Tco', covariant=True)
 
@@ -14,11 +14,14 @@ class type:
     def __call__(self, *a: object) -> object: pass
 class tuple(Sequence[Tco], Generic[Tco]):
     def __new__(cls: Type[T], iterable: Iterable[Tco] = ...) -> T: ...
+    @override
     def __iter__(self) -> Iterator[Tco]: pass
     def __contains__(self, item: object) -> bool: pass
     @overload
+    @override
     def __getitem__(self, x: int) -> Tco: pass
     @overload
+    @override
     def __getitem__(self, x: slice) -> Tuple[Tco, ...]: ...
     def __mul__(self, n: int) -> Tuple[Tco, ...]: pass
     def __rmul__(self, n: int) -> Tuple[Tco, ...]: pass
@@ -41,10 +44,13 @@ class bytearray: pass
 
 class list(Sequence[T], Generic[T]):
     @overload
+    @override
     def __getitem__(self, i: int) -> T: ...
     @overload
+    @override
     def __getitem__(self, s: slice) -> list[T]: ...
     def __contains__(self, item: object) -> bool: ...
+    @override
     def __iter__(self) -> Iterator[T]: ...
 
 def isinstance(x: object, t: type) -> bool: pass
diff --git a/test-data/unit/fixtures/typing-medium.pyi b/test-data/unit/fixtures/typing-medium.pyi
index 03be1d0a664d..cbb210283a50 100644
--- a/test-data/unit/fixtures/typing-medium.pyi
+++ b/test-data/unit/fixtures/typing-medium.pyi
@@ -6,6 +6,8 @@
 # Many of the definitions have special handling in the type checker, so they
 # can just be initialized to anything.
 
+from typing_extensions import override
+
 cast = 0
 overload = 0
 Any = 0
@@ -49,6 +51,7 @@ class Iterator(Iterable[T_co], Protocol):
     def __next__(self) -> T_co: pass
 
 class Generator(Iterator[T], Generic[T, U, V]):
+    @override
     def __iter__(self) -> 'Generator[T, U, V]': pass
 
 class Sequence(Iterable[T_co]):
diff --git a/test-data/unit/fixtures/typing-typeddict.pyi b/test-data/unit/fixtures/typing-typeddict.pyi
index 24a2f1328981..79afebb8e3d1 100644
--- a/test-data/unit/fixtures/typing-typeddict.pyi
+++ b/test-data/unit/fixtures/typing-typeddict.pyi
@@ -7,6 +7,7 @@
 # can just be initialized to anything.
 
 from abc import ABCMeta
+from typing_extensions import override
 
 cast = 0
 assert_type = 0
@@ -63,6 +64,7 @@ class Mapping(Iterable[T], Generic[T, T_co], metaclass=ABCMeta):
 class _TypedDict(Mapping[str, object]):
     # Needed to make this class non-abstract. It is explicitly declared abstract in
     # typeshed, but we don't want to import abc here, as it would slow down the tests.
+    @override
     def __iter__(self) -> Iterator[str]: ...
     def copy(self: T) -> T: ...
     # Using NoReturn so that only calls using the plugin hook can go through.