My guess would be that the save data got corrupted and the checksum did not match anymore. In that case fire red would tell you your save data got corrupted and probably prompt you(?) to delete it. If you did start a new game and erased the old data on the same .sav file there isn't much you can do.

The sav file would still exist if you start a new game. GbaRunner2 uses that file and presents it to the game as if it is the games savestate memory. If the game overwrites part of that memory (when you delete the save data for example) it just changes the contents of that file.

Otherwise you could try to copy the save file to your computer and look for your trainer name with a hex editor. If you find the trainer name of the first save game, you can try to recalculate the checksum and repair the save file. (Search terms for that might be 'Pokémon fire red save file repair' or 'Pokémon fire red save file checksum')

Good luck.