How can I stop Python from ruing deleted files?

I'm ruing files using shell_exec from PHP if that matters.
I'm ruing files in the pyshared folder, no package or subfolders.

My problem is that Python wasn't seeing code changes.
It's throwing errors that were written before and deleted in the changes made.
I finally deleted all the files involved. Python ran them anyway.
I rebooted - no help.
I looked in the __pycache__ folder and found all but the file called from PHP.
The file throwing the error doesn't exist in the pyshared folder...

How can I stop Python from ruing deleted files?