[kyteflyer]

You can delete from your iPad, not itunes. Go into iBooks, choose edit, select all, Delete. Worked for me.

The problem is that every book you ever downloaded will always be available to you in the book store. Until the last ibooks update you were stuck with those being listed. Now, you arent. You're not deleting them from your account, just deleting reference to them on your iPad (and thus, itunes)