Problem syncing book downloaded using iBooks
Authorize your Computer

I'm fairly certain that your issue is that your computer is not authorized with the Apple ID used to buy the iBook.  Therefore when you synced, the book was not transferred and then the iPad was synced. (Book basically deleted, sorry)

The fix is fairly simple, I believe you should be able to redownload your iBook for free, per Apple's new rules with previous purchases.  Then authorize your computer. From the Store menu in the iTunes menu bar, choose "Authorize This Computer".  Type in your account info, and then sync your computer/iPad.

Hope that works! :)