Q: I recently synced my iPad and lost all my iBooks. I think this may be because they were purchased on an old iCloud account but how do I get them back?

Updating the primary email address on an account should not affect any of its purchases, they will only potentially not show in the Purchased tab in the iBooks app for redownloading if the publisher/rights-holder has removed them from the store, if you've moved countries since buying them, or if you've hidden them : Hide and unhide purchases in iTunes or iBooks on your Mac or PC - Apple Support (you've checked to see if you have a hidden section on your account with those books in it ?)

If you created a new iTunes account you will need to use the old account to potentially redownload them (which might cause a 90 day association to that account : Manage your associated devices in iTunes - Apple Support)