Emulation Missing saves?

[Revenge24]

I haven't played my VBA for a few months, but I went back to it today to find that the saves I had for the games were gone. I tried all the games that I had saves for, and none worked. I always use Shift-F1 to save my games, so could this be the root of the problem? This also isn't the first time this has happened, I've had to restart games quite a lot in the past because of this. If someone can tell me what this is and how to avoid it happening, that would be great, thanks.