I'd like to point out that i was backing up my save file constantly with this game.
I realized it was eeprom that was chosen, so i used this tool
http://krikzz.com/forum/index.php?topic=1396.0 to change the save file to sram. just open the file, uncheck both the boxes on the right, chose SRAM, then hit ok. change the file name to .sra from .eep and then follow the directions below to boot using sram.
Just thought i'd share my findings here... i was playing the Donkey Kong [F2] and didnt hit force save type. using 2.04.
apparently to force the save type properly you have to hit A button on the game, hit select game only. then hit z button. hit opions. hit A button on save type until it goes to SRAM. hit b to back out until you are at the rom list. then hit start to start the game that was selected. (instead of hitting a on donkey kong, then start game, which will make it eeprom)
i managed to get my game to show up after converting to sram. i have no idea if it will delete it, but i am hoping i dodged a bullet/