If it still won't work you could try a different pc maybe. Some friend or a laptop or whatever. See if it still won't work.

Appreciate the support. I'll probably plink at it some more tonight. If I figure it out, I'll def be back to make sure the next guy doesn't get lost where I did.

Potentially it could be saved in the same folder as the rom.

Nope. I'm on Windows which has the file marked as "in use by Retroarch".

The part that has me baffled is where the new save file is coming from. That says to me that save state must be written somewhere else (my instinct says the ROM file itself, but someone else was saying that's patently wrong).

Fwiw, I've also tried playing with the save states (made backup copies first). If you hard exit, it saves off a copy of the current game state ("auto" slot), then attempts to open that up when I boot up the game. My current working theory is that the save file is regenerated from the save states when I try to load into a save state.

Any experiences that agree/disagree with what I'm seeing?

And can you delete it while playing the game?

So deleted the corresponding save file....but it just regenerates when i boot up the game. Its the same file I just deleted (even ran some hashes on it).

Right. I've only played till soul silver of the "real' games and I'm pretty sure Soul Silver is the only one that has that "feature"

Its not something the hacker built in. Apparently the instructions were included in the paper booklet that came with the game. Just pulled up a soft copy and the instructions are on page 10.

Maybe I didn't make this clear: by default, in ANY Pokemon game you shouldn't need to erase the existing save to overwrite it with a new save. The whole "erase" option was really only for if you were selling the game I guess. Whatever you find regarding that isn't really applicable to your situation.

Whether the save is from a different "run" or not you should just get the same prompt as normal asking you if you're sure you want to overwrite the existing save.

Unless the rom hack maker did something absurd, the issue you have is something to do with things outside of the emulated game. That being the emulator, its settings, or folder/file permissions on where the saves are being stored as files.

Pokemon should always allow you to overwrite existing save data. It just asks you to confirm you're sure before you overwrite.

It looks like for a little bit in the Nintendo DS era, they were looking to make that erasure more difficult (I'm not going to postulate as to why). For HG/SS you had to return to title screen and hold up + SELECT + B and that would take you to a hidden menu for deleting save data. (Forum board explaining the steps, as proof)

Obv this won't work in my case since I can't return to game once I hit the title screen.

Also, the save data isn't baked into the ROM. Save files and save states are stored as separate files from the rom itself.

I was not aware of this. Thanks for pointing me in a direction!

You can try to manually delete the save game. It's in the ./saves folder of retroarch. Don't delete the files in the ./states folder, as these are your save states.

If that didn't do it, you might need to change permissions for the folder.

What? Pokemon should always allow you to overwrite existing save data. It just asks you to confirm you're sure before you overwrite. That's been a thing since gen 1.

Also, the save data isn't baked into the ROM. Save files and save states are stored as separate files from the rom itself.

It sounds more like RetroArch doesn't have rights to overwrite files wherever you have your save data saving to. Or maybe you set that particular file to read only.

Edit: there may also be an issue with compatibility with the romhack and the emulation core. It's unlikely, but around 8 years ago I think I remember there being some issues with DS emulation and certain Pokemon romhacks. Best to make sure retroarch and your cores are up to date.