I think I'll add to this since I had the same thing happen to me today and the multi-boot method didn't work for me. I'm using EZFLASH Omega DE with Simplelight.
Fortunately, I used the EZFLASH Boot with Addon and used the L+R+Select and SAVE in conjuction with in-game saves. Never can be too safe. Anyway, I could still load my game from there but not from the in-game save. So what I did was load the game with Boot with Addon, used L+R+Select and LOAD to load save. Opened in-game menu and saved to 2nd save slot there (there are 3). I closed the game, reopened it, and this time, I went ahead and created a new game. I went through the intro until I could save (once Mumbo sends you to the past), and saved. I closed the game, reopened, and this time, I was able to select CONTINUE and saw new game I'd just made in slot 1, and now, suddenly, the save I'd made from before to slot 2 appeared with all my progress and everything. I went ahead and saved again to be sure, restarted, and my slot 2 save remained. Good to go.
I'll go ahead and disclaim that I'd manually deleted the .sav file from SAVER beforehand thinking that would wipe the issue and let me copy the backup I'd made back and it just work, but that unecessary apparently and maybe I don't know how saves actually work in this system (somehow still).
Also, when I looked into the SAVER folder I saw a file identical to the Grunty's save file but with a .mde extension. In another forum someone said this may indicate corruption but I ran a scan and found no errors on card. I went ahead and deleted that and backed up the SAVER folder to PC anyway. In any case, this solved my missing in-game saves with Grunty's Revenge. At least for now.