I just got a new hard drive and I want to sync all my iPad stuff back into my iTunes but it's just asking to erase the iPad. I just want all my books and stuff to be back in my iTunes.
As I referred to in the comment:
This copies over everything you purchased using the iTMS, App store, and iBooks.
For all content you put on the device that you purchased/received elsewhere, the process is a bit more complicated. Here are some suggestions:
Hope this is enough to get you going. Best of luck!
If you restore the hard drive from a Time Machine backup it should copy the invisible folder that is required so you won't have to nuke & restore your iPad. The folder you need to restore is "/Users/Shared/SC Info". I'm not sure how to easily restore an invisible folder. You could try restoring the whole "/Users/Shared" if you have a Time Machine backup.