Daemon mode mypy checks way more files the second time with the same command run

Bug Report

Daemon mode mypy takes a long time to check the same file with no modifications done

To Reproduce

git clone https://github.com/Ryang20718/mypy-repro
cd mypy-repro
python3 -m venv .venv
pip install -r requirements.txt
dmypy run example/c.py
dmypy run example/c.py

Expected Behavior

I'd expect dmypy to report no issues both times, but it hangs the second time

Actual Behavior

based on the timing file, we see time spent on numpy

(.venv)mypyrepro ryang$ dmypy run example/c.py 
Daemon started
Success: no issues found in 1 source file
(.venv) mypyrepro ryang$ dmypy run example/c.py 
Success: no issues found in 1087 source files

Your Environment

• Mypy version used: 1.10.0
• Mypy command-line flags: dmypy run example/c.py
• Mypy configuration options from mypy.ini https://github.com/Ryang20718/mypy-repro/blob/main/.mypy.ini
• Python version used: 3.10

Reproduce the issue with the listed virtualenv, mypy.ini, and repeated dmypy run example/c.py commands. Compare the first and second runs, including the timing file and unexpected numpy checks, then trace the daemon's incremental work. Done means the unchanged second command checks only the requested file and reports the expected result without the long delay.