diff --git a/mypy/dmypy_server.py b/mypy/dmypy_server.py
index c742f31164025..631aab4ccbc82 100644
--- a/mypy/dmypy_server.py
+++ b/mypy/dmypy_server.py
@@ -330,7 +330,7 @@ def cmd_run(
                         header=argparse.SUPPRESS,
                     )
             # Signal that we need to restart if the options have changed
-            if self.options_snapshot != options.snapshot():
+            if not options.compare_stable(self.options_snapshot):
                 return {"restart": "configuration changed"}
             if __version__ != version:
                 return {"restart": "mypy version changed"}
diff --git a/mypy/errorcodes.py b/mypy/errorcodes.py
index 50a82be9816d5..e87b04b6f4738 100644
--- a/mypy/errorcodes.py
+++ b/mypy/errorcodes.py
@@ -37,6 +37,14 @@ def __init__(
     def __str__(self) -> str:
         return f"<ErrorCode {self.code}>"
 
+    def __eq__(self, other: object) -> bool:
+        if not isinstance(other, ErrorCode):
+            return False
+        return self.code == other.code
+
+    def __hash__(self) -> int:
+        return hash((self.code,))
+
 
 ATTR_DEFINED: Final = ErrorCode("attr-defined", "Check that attribute exists", "General")
 NAME_DEFINED: Final = ErrorCode("name-defined", "Check that name is defined", "General")
diff --git a/mypy/options.py b/mypy/options.py
index 45591597ba69e..2785d2034c540 100644
--- a/mypy/options.py
+++ b/mypy/options.py
@@ -373,7 +373,7 @@ def use_or_syntax(self) -> bool:
     def new_semantic_analyzer(self) -> bool:
         return True
 
-    def snapshot(self) -> object:
+    def snapshot(self) -> dict[str, object]:
         """Produce a comparable snapshot of this Option"""
         # Under mypyc, we don't have a __dict__, so we need to do worse things.
         d = dict(getattr(self, "__dict__", ()))
@@ -388,6 +388,7 @@ def __repr__(self) -> str:
         return f"Options({pprint.pformat(self.snapshot())})"
 
     def apply_changes(self, changes: dict[str, object]) -> Options:
+        # Note: effects of this method *must* be idempotent.
         new_options = Options()
         # Under mypyc, we don't have a __dict__, so we need to do worse things.
         replace_object_state(new_options, self, copy_dict=True)
@@ -413,6 +414,17 @@ def apply_changes(self, changes: dict[str, object]) -> Options:
 
         return new_options
 
+    def compare_stable(self, other_snapshot: dict[str, object]) -> bool:
+        """Compare options in a way that is stable for snapshot() -> apply_changes() roundtrip.
+
+        This is needed because apply_changes() has non-trivial effects for some flags, so
+        Options().apply_changes(options.snapshot()) may result in a (slightly) different object.
+        """
+        return (
+            Options().apply_changes(self.snapshot()).snapshot()
+            == Options().apply_changes(other_snapshot).snapshot()
+        )
+
     def build_per_module_cache(self) -> None:
         self._per_module_cache = {}
 
diff --git a/test-data/unit/daemon.test b/test-data/unit/daemon.test
index c60068a44bece..424fc6d2b167b 100644
--- a/test-data/unit/daemon.test
+++ b/test-data/unit/daemon.test
@@ -28,6 +28,33 @@ Daemon stopped
 [file foo.py]
 def f(): pass
 
+[case testDaemonRunIgnoreMissingImports]
+$ dmypy run -- foo.py --follow-imports=error --ignore-missing-imports
+Daemon started
+Success: no issues found in 1 source file
+$ dmypy stop
+Daemon stopped
+[file foo.py]
+def f(): pass
+
+[case testDaemonRunErrorCodes]
+$ dmypy run -- foo.py --follow-imports=error --disable-error-code=type-abstract
+Daemon started
+Success: no issues found in 1 source file
+$ dmypy stop
+Daemon stopped
+[file foo.py]
+def f(): pass
+
+[case testDaemonRunCombinedOptions]
+$ dmypy run -- foo.py --follow-imports=error --ignore-missing-imports --disable-error-code=type-abstract
+Daemon started
+Success: no issues found in 1 source file
+$ dmypy stop
+Daemon stopped
+[file foo.py]
+def f(): pass
+
 [case testDaemonIgnoreConfigFiles]
 $ dmypy start -- --follow-imports=error
 Daemon started