Try playing the game for a while to see if it fixes, but you probably should have heeded the advice above. Also, see this article for further details: Savefile or savestate. This means that you will have to use save points within the game. These are likely to survive between emulator versions. Savestate compatibility is preserved wherever possible, but it is not always possible. Consult the manual for details on how to do this for your platform.
If you want to fix it yourself, you may need to manually specify the correct save type for your game.
