I've created an extension for flash that will allow you to auto-save and auto-archive your documents.
SAFE, Sequential Archive File Extension, will allow you to automatically save and archive your flash documents while you are working. Each document can be set separately. Auto-Archive will create a backup copy of your document with a time and date stamp.
If you're interested in testing it out, you can find the newest version here:
Please let me know what you think.