Sounds to me as if some of the content wasn't replaced properly.
I'd suggest deleting the entire file set on the server, then copying the fresh set over.
That worked!!!! Thanks so much for your help and for the quick response!
Also, if it happens again, try clearing your browser cache, closing all your browser windows, waiting 5min and trying again. (I don't know why waiting 5 min helps, as clearing your cache should be instant, but it generally does.)
I've found server caching to be particularly 'sticky' recently. (EDIT: particularly around the ToC, which will show old entries and not synchronise correctly, as you described)