What about an auto save like this:

• Every x minutes the current (modified) project is saved into a special file beside the project file (e.g. called {file name} + "~"). As long as the responsible timer is using the Swing-Thread, no side effects should occur, since afaik all modification is done in that thread.
• When you close or save a project, that autosave file is deleted.
• On opening a project where an autosave file exists, the program offers to open that file instead of the old one.

I know, that wouldn't help loading files destroyed by the save procedure, but at least crashed projects could be recreated.