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!
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.