If you've changed any of the filenames, that would cause deletions. Changing the author will change the directory tree. Changing the title will change the directory for that book. So then you get the OPF, cover, and any book files in those directories to be deleted.
As for the software you are using to sync, I highly recommend you switch to using
FreeFileSync. It's open source and done not have a version for purchase. It's excellent and well supported.