Whenever an iPhone is synchronised with iTunes, iTunes makes a backup of (most of) the iPhone’s data. You can view the iTunes’ backup history by going to Preferences > Devices.
iTunes maintains some kind of history for successive backups, but I have no idea of the underlying logic. You would imagine that three or four backups would be queued and older backups retired as new ones are made. But no, that doesn’t happen. Instead iTunes seems to purge its backup history on a schedule of its own devising — I’m guessing maybe daily, but I haven’t yet bothered to try and find out.
The problem is that when something goes screwy with your iPhone or iPod Touch (like erasing your contacts during a Google Mobile Sync…) and you fire up iTunes to restore it from a backup you now to be good, you can bet that the backup will have been purged.
Rebuilding your iPhone set-up from scratch isn’t a huge problem, but it is a time consuming one — installed apps are maintained as a separate list and your music should be on your computer, but you will have lost any custom settings and app layouts.
There isn’t an easy way around this, but there is a way around it — just manually backup your iPhone backups, either periodically or just before you do something that may put your iPhone data at risk.
Backing up an iTunes iPhone backup is simply a matter of copying it from iTunes default location to somewhere else. Which leads us onto the title of this post. Here’s where iTunes stores iPhone backups in all the operating systems it works with:
Mac OS: ~/Library/Application Support/MobileSync/Backup Windows XP: %AppData%\Apple Computer\MobileSync\Backup Windows Vista: %AppData%\Roaming\Apple Computer\MobileSync\Backup Windows 7: %AppData%\Roaming\Apple Computer\MobileSync\Backup
iPhone/iPod Touch backups take the form of hundreds of .mdbackup files, but they’re all contained within a single cryptically named folder — just copy it to the Desktop or somewhere, then copy it back to its original location when you need to restore it.
More info on iTunes synchronisation and backups over at the Apple support site.