Calibre emptying pdf files

[Manichean]

Originally Posted by kidpixo

Note that in step 2 I meant "I moved the pdf file from /somewhere/ to the folder where Calibre stored the old file in the file system".

This exact step here is the problem: You copy a file to a place where Calibre itself will try to copy it to, then you instruct Calibre to add said copy to its database, which results in it trying to copy the file onto itself, breaking things in the progress.

I can only reiterate the advice: Keep out of the library directory tree at all times and for all purposes. Otherwise, things go bad.