Thanks for your help. I reloaded the books each letter of the alphabet at a time. I found 1 book in the M's that caused the issues.
After each upload, I let the Kobo process the content, plug it back into the computer, delete the ghost files and then did the next set.
I think though, if that one file hadn't have been bad it would have loaded up correctly. Whew! what a pain. Thanks for your tips, they really helped