Whatever folder you open the rom from, there will be a .3DN file and a .BAK file. (Well, there will be assuming you've saved the 3DN twice)
The first time you save a 3DN file, it creates a ".3DN" file. The second time you send a 3DN, it creates a new ".3DN" file and the old ".3DN" is saved as ".BAK". This is a nice backup feature, but it only serves as a safety feature for one save. I don't believe this was covered at all in the manual yet, so don't feel dumb that you didn't know about it. I wrote a whole suggestion post to create a more complex backup system than this, not even realizing that the emu's creator already had this basic version already in it.
If you weren't aware of the .BAK file, I'm wiling to bet that at one point it was about 8MB itself, but if you've saved the 3DN twice with no work done on it since then, it's probably only around 400kb again.
if you still have your own saved backup file, try uploading it and posting a link here and I'll try using it myself. I'm not familiar with the game. Is this the Famicom version of Castlevania?