If i remember correctly it was a part of a "general debugging" attempt. Early in the FreeCAD migration from PPA to Conda. Anyway, i somehow feel this isn't .pyc files, or general related issue, but best to wait first for @Genues respond.
When it comes to .pyc files, as we are already talking about them, we can decide further, on the managing strategy. We can include them in AppImage, the ones created in Conda environment, delete them and use an environment variable PYTHONDONTWRITEBYTECODE, starting with Python 3.8 to delete them and tryout the usage of use the environment variable PYTHONPYCACHEPREFIX.
Therefore i would suggest for first to wait for the @Genues respond and feedback. If the issue persists, we should delete the .pyc files once more and add PYTHONDONTWRITEBYTECODE environment variable. If the issue will persist, it's likely not a .pyc file related issue.