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One way to fix your saves is to use VBA-M: https://github.com/visualboyadvance-m/visualboyadvance-m/releases Download the emulator and on the menu select: Options > Emulator > Save Type and change this to Flash 128k. Now name the save you wish to fix the same as your rom, example: Emerald.gba and Emerald.sav and ensure these are in the same folder. Load the Emerald rom in VBA-M, continue the game and save. If you look at the save again it will now be 128k and work fine with PKHeX. (You should be able to load your save state also, save in game and Emerald.sav will be a 128k save of that save state)

Read the sticky in the parent forum. http://projectpokemon.org/forums/showthread.php?24589-B2W2-General-ROM-Info /a/0/0/4 ********* sprites (pokegra)