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.