Interesting. So I was testing the save with my dumped ROM from Emerald in mGBA. The save that was on the cart loads fine, but when I load the save dumped from PKHeX I get the corrupted save error message. I can confirm that the ROM is copied from a legitimate game, and that is why I wanted to test the save on the ROM in mGBA first. I will try to dump the legit ROM again to make sure it all copied over correctly. Should I just try and copy the sav directly to the cart? Is there potentially a known issue with mGBA and PKHeX that I am missing?
Okay, I have an update. I decided to load the save file to the legit cart and the same corrupt data error message appeared. However, the legit cart was able to load from the previous save, which is the same save I dumped from the bootleg cart. My guess mGBA does not have the ability to repair the save by loading from the "previous save". Everything seems to be working fine now. Thank you for your fantastic tool!