Simple recommendation would be to get a few CD-RWs and make a few cheap "v1.0" backups. This way, if you lose them later on, you can still have a CD with them on it. When you update your source and things all look good, verify the source on the machine, erase (format) the current CD-RW and burn a new copy. If you have SourceSafe (I think that's it) for MS, you can check your stuff in and have your own CVS-esque tree otherwise you could use CVS and CVSWeb on a linux box to make sure you keep integrity and all tracked changes intact.
Also, what methods (other than more frequent backups) can I use to protect my files from deletion without this problem occuring again?