Do PDF documents in iBooks get backed up to iCloud?
It is very strange that there is no answer to this on official Apple forums. Searching for this online often brings up Wifi iTunes sync or using file sharing services like box.net to do this.
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Yes, as long as you have the iCloud backup enabled your documents will be backed up. I have first hand experience. After exchanging a defective iPad the new one, after entering my iCloud account information, had all my books (both epub and pdfs, I don't buy books from the iTunes store because of DRM), links, gamecenter data, and application data.
What didn't synchronise was music and videos.
Based on my tests, PDF files and non-iTunes store eBook content are backed up to iCloud. However, Video and music files not purchased through the iTunes Store are not backed up to iCloud. (For this discussion I'm ignoring music backed up using the premium iTunes Match service.) These media files are synchronized with (and presumably backed up from) an iTunes library attached to a computer.
Apple doesn't specifically call out PDF files in iBooks, but they do provide some reference: iCloud: Backup and restore overview
You get unlimited free storage for:
Purchased music, TV shows, apps, and books *
You get 5GB of free iCloud storage for:
Photos and videos in the Camera Roll Device settings (for example: Phone Favorites, Wallpaper, and Mail, Contacts, Calendar accounts) App data Home screen and app organization Messages (iMessage, SMS, and MMS) Ringtones
The following items are not backed up to iCloud. You can sync these items with a computer using iTunes:
Music and TV shows not purchased from the iTunes Store Movies, podcasts, and audio books Photos that were originally synced from your computer