In both the Freak and the Retron5, changing cheats invalidates save files. Perhaps the new firmware corrupted it?
If you want to just delete the save to get the game to run, then activating a cheat could work. You can do so by adding a new entry to the cheat XML file, using the CRC of the game as reported by the game DB XML dump (menu option).
Recovering the save is another story... maybe you can back it up to a PC and see if FCEUX can read it.
It isn't the file that has gone bad; it's likely the save state data. Something happened between when I last played it and now. I'm honestly not sure if I added the ROM before or after I updated the console. Either way MMC5 is a complicated mapper and if any changes occured to the way it is implemented, the update may have broken my existing save state.
Every time you exit the game, it creates a save state. Every time you reload the game, it resumes from the previous save state. There is a Reset command that allows you to reset the emulated system, but I believe this acts as a soft reset and not a hard one. I cannot for the life of me figure out how to load a ROM without also loading the save state, if one exists. And soft reset and hard reset are different. For instance, Super Mairo Brothster retains the high score when you hit reset on your NES. If you rescued the princess, hitting reset will still give you the second quest. It was a common issue with Nitnendo's Virtual Console on Wii for people who beat Super Mario Brothers once and wanted to play the first quest. Nintendo's workaround was to power off the system without exiting the VC emulator. I could try disconnecting the Retro Freak power adapter while the game is running but I don't want to break something.
Anyway, I've decided to delete the Naked Peach ROM and use the IPS patch directly on the RetroFreak's own dump from my personal copy of Super Mario Brothers. Regardless, the lack of an option to cold boot the game without loading the existing save state is bothersome. Since the save states are stored on the Retro Freak's internal memory, and there is currently no option for viewing or deleting the internal save states (you can currently only view snapshots and SRAM saves - This particular hack does not use SRAM) or transferring them to SD card.
EDIT: Patch worked. You need to create a special folder in the Retro Freak directory on the SD card titled "Patch." Throwing IPS files in the games directory does not work. As for backdoor ROM loading, I'm keeping my Retro Freak mostly clean and piracy free, save for a couple homebrews that won't dump, and a couple Supergrafx titles...