Update: I rolled back to the immediately previous 3dn file where I had completed 3 Robot Master stages instead of 4. I re-did Metal Man, and things seemed to be okay.
My new tactic is this:
- Do not save your work frequently.
- Finish a stage, or half a stage, depending on how much work it was.
- Save your 3dn
- Hard reboot (exit 3DNES)
- Load the game.
- If the 3dn file was corrupted, roll back to the last version, or even the one before that if you need to.
- If the 3dn file was not corrupted, change one thing and then hard reboot again. It's possible that the 3dn looks correct but is still corrupted.
So far I've finished all eight RM stages and two Wily stages, and have set the Wily Fortress image. I did get corruptions partway and had to re-do Wily 1, but I'm worried that saving super frequently increases your chances of getting the bug, and you won't know until you hard reboot.