Pkhex not saving

[Cheesestxsss]

I've been trying to change stuff/add pokemon using pkhex. I've made sure to save and set everything, double checking by closing pkhex after exporting the file and re opening it to see if everything is still there, which it is. But when i open my game, Legends za, I see that none of my changes are there. I don't know what the issue could be, and i would appreciate some help.