Daemonized mypy ignores errors on files that previously passed (cache bug)

Bug Report
dmypy is failing to notice type errors when they are introduced into a file that has already passed type checking. I'm observing this even on extremely minimal examples. It seems like once a file passes checks once it is never checked again by dmypy.

Specifically, this seems to happen when dmypy is given a package. Explicitly passing the filename still gives the expected errors.

To Reproduce
Create a package called test_package containing an empty __init__.py and a file called test.py with the contents:

a: int = 1
b: int = "foo"

Run the following commands:

$ dmypy run -- -p test_package
test_package/test.py:2: error: Incompatible types in assignment (expression has type "str", variable has type "int")  [assignment]
Found 1 error in 1 file (checked 2 source files)

# Comment out line 2 of test.py

$ dmypy run -- -p test_package
Success: no issues found in 2 source files

# Uncomment line 2 of test.py

$ dmypy run -- -p test_package
Success: no issues found in 2 source files

Expected Behavior
The last command should raise the "Incompatible types in assignment" error.

Actual Behavior
No issues are found, despite the contents of test.py being exactly the same as the first run.

Your Environment

• Mypy version used: 1.13.0
• Mypy command-line flags: (see examples above)
• Mypy configuration options from mypy.ini (and other config files): None
• Python version used: 3.11.6

Reproduce the issue with dmypy run -- -p test_package using test_package/init.py and test_package/test.py, then inspect the daemon's package checking and cache behavior. Confirm that after commenting and uncommenting the assignment, the final run reports the incompatible types error again.