I've been updating my iPad with Apps from my home desktop (Mac Pro). At work today, synced it up to the MBP (my "work" laptop), to get my calendar merged, and when the notification popped up to "sync Apps to this iTunes?" (something like that), I checked No, because I didn't want my 1.75GB Elements stored on my laptop, and the countless other Apps I don't need backed up in two places. Well, iTunes backed up my iPad (something it seems to be doing constantly), and then when I had access to the iPad again—all Apps were deleted. Including GoodReader, and all the PDFs I'd synced from my Mac Pro to the iPad. And iBooks (w/ all books). After a bit (I know I can just go back home and re-sync my Apps, or at the very least re-download them, and re-sync all the PDFs), and re-download all the free books I got from iBooks... I unchecked "sync apps" on my laptop's iTunes. #@($*()#$&*^~! You need to do something about this, Apple. For being so user-friendly, "syncing/deleting" all your apps like this shouldn't be so easy to do. SUMMARY: Do not sync apps to two iTunes, uncheck "sync apps" from one of them in the iTunes preferences. That is, if you don't want your apps backed up in two places.