
This always sucks. To prevent this happening to YOU, you'll want to download powerful program by 2BrightSparks called SyncBack. It might look intimidating at first, but once you get the hang of it, it's quite actually quite simple.
The premise of it is that you create "profiles" which are instructions on the kind of backup or synchronization that you can do. Create as many profiles as you want. You set the source and destination, and you can schedule the backups as well. Other features include which subdirectories to backup, filters, as well as more advanced features like FTP, email backup, and compression.
The free version of SyncBack is very versatile, but there is a Pro version which packs in much more. It's definitely worth it, and it saved me on many occasions. The backups run in the background without interrupting you, and only run when scheduled.