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Calibre is very careful when moving files.
Copy first, then delete. If there was any problems with the copy, that would crash calibre or generate an error, before the delete. So I still say that it isn't calibre that caused your problems. If it was thousands would have reported problems a long time ago and it would have been fixed.
It is also unlikely to be a hardware error, since you seem to be able to use your computer and the harddrives.
Unfortunately that only(?) leaves user error. That you yourself somehow inadvertently deleted the books. At times like that it is good to have recent backups.
I don't trust myself or hardware, so I let my computer automatically backup my calibre library (and other stuff I don't want to loose) every hour to an extra harddrive on my computer, and daily to a NAS with redundancy. And to external USB hard drives now and then. And I have most of my library on my reading device. But I do trust calibre to not delete any books, unless I tell it to.
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