I have an iPad with nearly 1,100 pdf books on it (stored in iBooks) which I've obtained from scouring the web for the past year, and which contains owners manuals, users manuals, presentations, books, white papers, and even personal documents of mine. I had been syncing these pdfs to my desktop with iTunes periodically, and backing them up to DVD about quarterly. Apple doesn't have a "Backup iTunes" option (Stupid Apple), so I was backing up my iTunes folder with all its music and books. Then my desktop with iTunes on it crashed, and I had to rebuild the desktop from scratch and reinstall iTunes. That was fine, as I had a backup of all the iTunes music and such. However, I had an older backup of my iBook pdfs, so was going to lose a couple of hundred books by restoring from my DVD of books. Also, I already had my iBooks on my iPad categorized the way I wanted them, as I had built libraries for each topic, and stored the books accordingly. I didn't want to have to go through the pain to reorganize all the books I had, and then find the books I lost. This would mean hours of lost time, to get back the books and categories that I currently had on my iPad but couldn't get into iTunes. That is because when you sync a iPad to iTunes, your only choices are "Erase and Sync" and "Transfer Purchases." "Erase and Sync" erases all the content of the iPad, and syncs it with the content in iTunes. That didn't work for me. "Transfer Purchases" didn't transfer any of my pdfs off of my iPad, so that didn't work for me at all either. (Stupid Apple!).
So I said F-it, and didn't sync my iPad, and just used it without syncing to iTunes. I hate iTunes anyway, so this was fine. This worked for a while, until my iPad ran into some sort of problem with adding new pdfs to my iBooks library. The symptoms where that when I'd open a pdf in Safari, and say open in iBooks, it would just barf and not add it (Stupid Apple!). Since I was no longer able to add any books to my iBooks library, I was left with little choice but to try to fix the problem.
I could have bought one of those programs to transfer off all of my pdfs, but then I'd lose my categorization. Also, I didn't want to spend money to pay to fix Apple's stupid implementation. So I thought I'd try backing up to iCloud, restoring my iPad, and restoring from the iCloud. (You can 'supposedly' get a full refund in 15 days). I had more books than the 5GB of free iCloud storage, so I paid $20 for more space. I then backed up my iPad books to iCloud. This took several hours, proving that it was backing up my pdfs.
I then tested if syncing (fricken "Erase and Sync") with iTunes would nuke all my pdfs... it did. Even after I Transferred Purchases and backed up my iPad to iTunes prior to a sync. I lost nearly all of my pdfs. Stupid Apple. Restoring from my restore point still left my pdf books missing. Grrrr. Stupid Apple!
Still, I had a backup of my pdfs on iCloud, so I went into my iPad settings, clicked on reset, and "Erase all Content and Settings," and held my breath. After my iPad came back, it was a fresh install--none of my settings. But when I set my iPad up, after I got the network settings set up I could restore from an iCloud backup. (Why Apple doesn't let you restore from a backup without nuking all your content is beyond me... Stupid Apple). So I selected "restore from iCloud" and waited half a day for the content to populate back to my iPad.
I tried to restore from iCloud, probably 20 or 30 times, and it failed with the unhelpful message "Restore Failed" or sometimes that it lost its network connection. But in all my restore attempts it seemed that it always died when the screen went to sleep. I held on to the iPad for an hour or two, always stopping it from falling asleep, and it was fine. But as soon as it went to sleep the restore failed. Stupid Apple seems to make you keep the screen active... for 10 HOURS! Now that is one of the stupidest things I've ever seen!
So, I had no choice... I went to sleep touching my iPad.... and when I woke up the restore had completed. Finally! I checked my iBooks, and all my pdfs were there, but without the normal cool cover (they had the default no graphics cover... just text).
I tried to sync my iPad to iTunes, and incredibly, it still just had the options "Erase and Sync" or "Transfer Purchases," where the pdfs wouldn't transfer! Arggghhh.
I tried to upload some new pdf books to iBooks, and that now seemed to be working. So at first I thought that all the pain was worth something. But then.... as I viewed the books and the cover art started populating, I tried again to test my suspicion that rendering the cover art corrupts iBooks. Sure enough, after I got about half of my cover art rendered, I could no longer add pdfs to my iBooks library!
So, I'm stuck where I was at the beginning of all my pain. I can't add any more pdfs to iBooks, I can't sync with iTunes or it will delete them, and I can't transfer them to iTunes. I guess I'll have to buy a third party software package to back them up.
Apple, if you're reading this:
1) fix your iBooks pdf cover art rendering engine. It is certainly flawed.
2) allow "Transfer Purchases" to transfer pdf books. It's stupid that you don't.
3) code your iCloud restore to not die when the screen goes to sleep
I'm going to recommend some other eReader to my friends. GoodReader seems pretty cool. It allows you to take notes and highlight the book. Heck, I'm looking strongly at the Galaxy Tab or other tablets. They won't stop me from downloading my books to my computer.
Also, I'm currently going through the refund process for my iCloud purchase. That also seems painful. If you are considering purchasing iCloud---don't. Apple makes it very hard to refund your purchase within the 15 days like they say they will. You can't email them, call them, or fill out any form. You have to submit a ticket (that you can't even specify what for) and wait for them to call you back. That is crazy!
They can't even get their grammar right! How about "Think differentLY!"
11 Oct 2012 Update: Apple recently did an iBooks application update, and I lost over 1200 books! Screw You Apple! I tried downloading "Transpod" to transfer them in case they were still on my iPad but iBooks didn't see them. But Transpod didn't see them either. Stupid Apple just deleted them with the iBooks application update! I tried to restore to a backup I had made and that, of course didn't back them up either. So I just lost 1200 books and tons of time.
I only hope that someone sues them for their lost books. I also hope that someone (Charlie Miller, are you listening?) pwns them because the cover art rendering mechanism on the iBooks application is clearly vulnerable. This is an easy way to pwn any iPad or iPhone, as it's included by Apple, and it is SO flawed.