i've never really used apple products, but my wife does the macbook iphone thing. we've had two experiences with it randomly deleting her shit.
first time (this was about a year ago, not sure what itunes version):
she got a new iphone, all was well. we wiped the old iphone. one day she dug up her old iphone, and decided to start using it to play music in her car. plugged it into the macbook.
itunes asked if she'd like to sync with the new device. she said yes. it deleted all of the music on her computer, including physical files.
plugged her new phone in, it acted as if it had never seen it before, and asked if she'd like to sync. it then deleted all of the music on her new phone as well.
she'd been using iphoto to organize all of her pictures (many thousands of them)
fired up iphoto one morning, and all of her shit was gone, it was like she'd never used iphoto in the first place.
no sign of the monolithic 'iphoto store' file, or anything. no original pictures. gone.
there are two things my wife loves, pictures and music, and it systematically fucked her entire collection without warning. unfortunately many of these items had not been backed up. these are just my observations, i don't know why it would do these things, and i don't care. i no longer trust that peice of shit operating system or any of its devices, and i use incremental backups of her entire laptop using rsync now (not time machine, i don't trust it either)