Have you tried this:
Connect the iPad with the books on it to iTunes. Then, on the iPad tab, right click and select "
transfer purchases." This should put the books on/in iTunes. You can check this by going to the Books tab and seeing they are there. For example, in this picture, I just put the first four books into iTunes from my iPad:
I had gotten those four books by downloading them out of my Calibre account in Dropbox; they are DRM-free and had nothing to do with iTunes, ever, until just now.
Then, eject the iPad and connect the new one. Navigate to the iPad's Books tab and check the "Sync Books" option at the top. Then under Books, you should see all the books that were transferred over from the other device. Put a check mark in the ones you want and then press the Apply button at the bottom right. The books will move over to the new device.
At least, this worked for me when I transferred those four books from my iPad over to my iPhone.
From what I can tell - and this is the key point - once you have transferred the books to iTunes, they are there until you choose to delete them from iTunes, so, it won't matter if you have them on your device(s) or not. Then, When you want them on a device, it's a matter of checking and syncing them over.
Now, when/if you restore or backup, these books may not be put back on. However, they will still be in iTunes so you can sync them back over. I do recommend you do the transferring and syncing before wiping the first iPad, just to make sure. I don't think anything can/will go wrong, but you never know...
Hope this helps.
Marilyn