If you have updated the IDE from the
update page, you'll never have the problem. It's like any software, if you're using a buggy version, it's your fault for not updating.
Personally, I have an SVN server set up on my PC (really easy to
install and set up).
Every time I make some changes that work, I add it to the SVN repository. When I backup, I only backup the SVN repository. This ensures a number of things:
No lost code.
Can
always revert to older code if you want.
When backing up, I'm guaranteed to not have it take too much space since I don't have erroneous binaries and what-not floating around (SVN is primarily source only).
Give it a shot, it'll save you headaches, and is as simple as Rightclick->Commit to add changes to the database.