[DNSB]

I'd suggest doing your transfer in smaller blocks, say, 512 books per block. When/if the transfer abends, break that block into 2 blocks and keep doing so until you have your problem book located closely enough to start checking individual books.

So 512, 256, 128, 64, 32, 16 <= at 16 is where I would check the books individually. For the epubs, I would suggest using either Sigil or calibre's editor with the epubcheck plugin for the testing. Though from your posted debug output, it seems that the problem files have issues with the mimetype file which should be uncompressed in the root of the epub's zip container.