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Pokemon Leaf Green VC save file export not working after Elite Four/Sevii Islands

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Hello, recently I have been playing through Pokemon Leaf Green on my New 2DS XL using an injected VC GBA rom. I have had no problems with my game other that having the pop up: "The save file is corrupted. The previous save file will be loaded." but it has not affected my save file. This is not the problem I am having here however.

I have exported my save file a few times using GodMode9 and the file has always worked until after I beat the Elite Four and the Sevii Islands. Whenever I try to use my save file after exporting it, I am always met with the message: "The save file has been deleted..." bringing me back to the very beginning where Professor Oak asks for my name and such. I have tried using the save file with mGBA and also injecting the save file into a different 3DS that has GodMode9, but they were met with the same thing.

Despite this though, my original save file on my 2DS works completely fine for some reason and I am unsure why this is happening. I was wondering if the corrupted message I've always got has something to do with this? I included my save file to see if anyone could figure out the issue I am having, I do not know how else to fix this. Thank you. 

Pokemon - Leaf Green Version (U) (V1.1).sav

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