I really hope I'm just missing something.
I've loaded the latest version of PKHex, gotten a save file from off my game, opened the save file in PXHex and got to work making changes. I only changed existing pokemon, giving them held items or changing their levels, all checked for legality. When I was done, I went to Export SAV -> Export main. I got the message that my file was saved. And then I was able to load everything into my game but I noticed that none of my changes were in place.
I went back to PKHex and opened the main file I had just exported and saw that it had absolutely none of my changes.
I've tried a couple different things; creating a new file instead of overwriting one, saving directly to my hard drive and not my SD card - none of these work. Instead of just editing stats for existing pokemon, I made a copy of one of them and then exported the SAV. I was surprised to see that the copied pokemon showed up in the main file, but none of the stat changes I made were saved. So it seems like the save is working, but only for making exact copies of existing pokemon.
Has anyone else experienced this?