Which game/3DN, and what was the date of the release of that 3DN in the repository.
Wwhat point does it say "Improper Format"? When you try to save the 3DN, or when you try to load the re-saved 3DN?
Also, which version release are you using?
This is possibly an issue I was worried might happen earlier, but did not want to bring up until it ever became a problem. I suspect you're trying to edit an older 3DN file that was created with an earlier version and it's not playing well with a more recent update of the emulator.