Wow. I've been doing a lot of ePub testing. I edit the XHTML and CSS. Zip an ePub. Copy it to iTunes. Hit Sync. Get bored with waiting the THREE ENDLESS MINUTESit takes to sync a tiny book file. I open the book, calculate the results of my test, go back to BBEdit and start over again.
And that's not counting keeping track of each ePub document.
But that wasn't enough. There must be some sort of caching going on, because even if I delete the ePub from inside the iPad and even if I delete the ePub from inside iTunes, and even if I wait those excruciatingly long 3 minutes for the thing to entirely sync up my tiny new ePub file, I wasn't seeing the changes that I had made.
What could be the problem? Well, the problem is the title. There must be some caching going on inside iBooks, I don't know. But if you try to upload and sync an ePub with the same title as an existing one (even if you had deleted the existing one!!), it will continue to see the old one.
The key is to change the title in the content.opf document. Then it works.
(And, you can cancel a sync right after the ePub is copied to the iPad and save 2.5 minutes.)