Some of my saves has saved as a .FLA instead of .eep, i tried converting them to .eep with notepad but were unsuccessful.
Games that this has happened witH: Paper Mario and Zelda: Majoras Mask
Not all N64 carts used the same chip to save, they used all sorts such as eeprom and flash (just like the GBA too). If you changed the save type, the game probably wouldn't boot so I would not touch it.