DW just works with the files on your system, it doesn't actually store them within itself. One of the more common troubleshooting steps is a complete uninstall/reinstall. Your files will be safe, wherever they're stored on your hard drive, as long as you didn't do something silly like put them inside DW within your Windows Program Files folder.
However, if you do reinstall, you won't be able to activate MX2004 with the old serial number you have on hand (if it's the one that came with the program). The Macromedia activation servers have been gone for many years, so you would need to use the steps and serial number from this help page:
Error, "Unable to Activate" in Macromedia legacy products
I decided to try a restore point from before I ran Hitman Pro... BINGO! It worked! No reinstall, no angst! Very relieved. Thank you all for your quick and willing help! 