When you select "Sync Books" with "All books" or "Selected books", it will tell you that it will erase all BOOKS, not Music on your iPad. What it means it that it will erase anything not checked in the Books section below. If you selected "All books" it will add any thing that's in the books that's not already on the iPad.
But because you are doing a sync of everything, if you have music, books or anything else that you downloaded to the iPad directly from iTunes on your iPad, they will be erased because it is syncing from iTunes to the iPad and these items aren't in iTunes yet. You must first go into itunes and click the "File" at the top left corner (tool bar) and select "Transfer Purchases from "your ipad name", this will transfer all those items that you purchased on the iPad to iTunes. Now select those new items in iTunes that you just uploaded and that you want on your iPad, then sync and everything should be there.
Remember it syncs FROM iTunes TO the iPad normally, however some things do seem to sync without all the fuss from the iPad to iTunes. So, just pretend it doesn't and always do the "Transfer Purchases from..." thing to be safe.
The safest thing to do is to always purchase and download to iTunes, not from the iPad directly, and then sync the iPad with iTunes. Also, downloading into iTunes is usually much faster and you don't have to worry about the size limits, 20mb I think, of downloading on the iPad.
The only other reason I can think of that it would try to remove music to download books, is if the iPad was full and it needed the space to put the books on it.