Losing saves is not a random issue, it happens for a reason and it very easy to figure out. The saves get a seemingly random name partly based on what number they are in the alphabetic order of roms on your SMC, if that order changes, the save is lost (or not actually lost, it is still there but won't be used). So what happens is that if you get a new game and put it in your gb directory (let's use castlevania as an example), all games with the letter C and lower will lose it saves. I cannot understand why it doesn't just name the save after the game, the current system is very badly thought out.