diff --git a/mypy/errors.py b/mypy/errors.py
index 2c2c1e5ca227..03eb4a6adf21 100644
--- a/mypy/errors.py
+++ b/mypy/errors.py
@@ -668,6 +668,8 @@ def generate_unused_ignore_errors(self, file: str) -> None:
                 False,
                 False,
                 False,
+                origin=(self.file, [line]),
+                target=self.target_module,
             )
             self._add_error_info(file, info)
 
@@ -720,6 +722,8 @@ def generate_ignore_without_code_errors(
                 False,
                 False,
                 False,
+                origin=(self.file, [line]),
+                target=self.target_module,
             )
             self._add_error_info(file, info)
 
diff --git a/mypy/server/update.py b/mypy/server/update.py
index 00b823c99dfd..e909840d2757 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()
@@ -1027,6 +1029,10 @@ 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 7586c8763d33..869f60b4e1fd 100644
--- a/test-data/unit/daemon.test
+++ b/test-data/unit/daemon.test
@@ -522,3 +522,92 @@ 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
+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
+Daemon started
+$ dmypy check -- bar.py
+bar.py:2: error: Unused "type: ignore" comment
+== Return code: 1
+$ {python} -c "print('\n')" >> 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
+$ {python} -c "print('\n')" >> 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