Chris,
As far as I know, when Word opens a file for editing, it opens the original file as READ-ONLY and opens a second file with the first letter of the filename changed to a "~". All changes are made to the "~" named file and when you close the file, word closes the "~" named file, deletes the original file then renames the "~" named file to the original file's filename. (I hope that made some sense. I just woke up!)
As long as you don't backup any files with "~" as the first letter, you should be fine.