Your Preferences folder tells Calibre what folder to use as the Current Library.
That is also (like Libraries)
not deleted, even if you uninstall Calibre.
You have a rogue app running (amok):
Disable any Cloud/NAS auto sync (calibre Library and Configuration should NEVER be 2-way. Mirror really should only be done when Calibre is shut down)
It maybe trying to put things back . (time keeping differences might confuse. Common with Win vs Linux)
You have an Anti-?? that thinks your book formats are bad
You are running a 'cleaner' that detected that the only registered app is gone and is tossing 'useless trash'
