I'm in the middle of working on Mega Man 2. I got to a point where I was confused about how to handle the graphics, so I wanted to load the one the community uploaded to see how they handled it.

I did the following:

1. Copied my 3dn file and saved it to the desktop
2. Copied my megaman2 rom to Mega Man 2 - Copy.nes
3. Downloaded the community 3dn file as Mega Man 2 - Copy.3dn
4. Loaded Mega Man 2 - Copy.nes just to see what I was looking for

When I loaded Mega Man 2.nes back up, the program acted as if my 3dn file wasn't working. I pasted my desktop's backup in, but that didn't work either. What's going on?

More info: I tried the following:

1. Re-downloaded the community file as Mega Man 2 community.3dn
2. Copied and pasted the rom as Mega Man 2 community.nes
3. Loaded that rom. The community file loads fine.
4. When I load my original work, it is rejected and the game appears to be default, as I described earlier.
5. Then, when I load the same community file again, it too fails and the game reverts to default!

I suspect the program is auto-saving 3dn information and it absolutely should not.

It auto-saves 3dn file for the old rom when you open a new rom. Up for now it doesn't check if the new rom is the same compared to the old one. It's really a potentially buggy behavior.

I don't think it should ever auto-save the 3dn because I think what happened to my file was that it auto-saved while closing (to open the other rom), which corrupted it.

You are using 1.0 or 1.1b1?

Could you send me your 3dn to identify the problem?