Homebrew Pokemon Sun not saving

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PandaPomf

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So I use JKSM to import my PKHeX Pokemon onto my game which works perfectly fine, the problem is when I, for example, re-beat the elite 4 again with my new Pokemon and save the game, go back onto PKHeX and put on more Pokemon, then finally go back to the game to find that it didn't save and I have to do the elite 4 again. My new Pokemon are on there but the game just doesn't properly save. I don't know really how to explain but I feel I'm missing something obvious here, help?
 
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