Unable to transfer to iMac books purchased using iPad

I have several books on the iPad that are not synced on my computer. I tried to sync the books using iTunes but I get a message saying that the books on the iPad will be replaced by the ones on my computer--to me, this means that they will be lost. Does anybody have an advice for me as to how I can backup/synch/transfer books from iPad to iMac??

My ultimate goal is to setup iPad to use iCloud and the ability to synch media (Inlcuding books) on all my devises. I need to update the iPad to v 5.1 (from 4.3.5) and I receive a notification that all media will be removed. I would like to keep the books purchased using the iPad though. I appreciate any ideas or help.