EDIT3: Ok, now I'm lost. I just had the same exact issue with my Japanese Red cartridge that I had with my U.S. Crystal.....ugh. Save got completely wiped. Back it up, PKHeX wouldn't read it, put cart back into GBC, now my save is deleted and can only do a New Game.....idk what's going on. It is, however, a different error message than Crystal. Added photo of new message. Also added the save file because I have no idea how to read hex editors.
EDIT2/FIX: Opened up my cartridge. Cleaned all the sticky residue off the battery with a pencil eraser, removed a possible short that may have been caused by a very small piece of leftover solder, and slightly tried to clean up the solder around the battery. Now PKHeX is actually reading my SAV for the first time. PKHeX now reads the SAV and writes to the cartridge just fine, as it should.
EDIT: Ok, so strangely, when I re-boot the game, it deletes my save file, but not every time I restart it. I just swapped the cartridge battery (again after doing so 6months ago) just to make sure it wasn't that, and it is still doing it every couple times I restart the game. However, I'm noticing it's only doing it after I take my Crystal game out of my cartridge dumping device (but again, not every time I take it out). Not sure if it's coincidence or what. I don't think it's the cart dumping device because I've been dumping my carts all day and none of the other games' save data were deleted. Help?
Just started a new game and got my starter. Saved then dumped cart but PKHeX is giving this error every time. Works fine with my Gold Version. These are physical cartridges. Both my Crystal and Gold saves are 32kb.
POKEMON RED.sav