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Turns out the files weren't ever "deleted" the pathway that the database used to find the files got disconnected somehow.
I use Calibre extensively on more than just one PC so having it mirrored and working within the cloud so to speak is a must.
Thanks for the suggestions and the python script!
Everything is working as normal now, and I'm only finding a book here or there that isn't in the library that I need to re-add.
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