iTunes wants to delete my books
The most maddening thing about iTunes is it's preference to delete things before. then, syncing them. 

One thing you can do now is to be sure and make a copy of your books folder, perhaps in Documents. You might also back that up to Dropbox. iCloud has not proven itself to be a reliable backup in the cloud, no matter that it syncs quite nicely.

Having said all this, I'm not sure where you are seeing the 2.5GB, and where the 750MB. Generally, one refers to books, or e-books. iBook is a reader, as is the Kindle app, for example. Calibri is, at present, the only real e-book manager for the Mac.