Save File Corrupted During Saving

[ThatsSoWitty]

So tonight, I using PKHex to clone a Pokemon so that I could give it to a friend and I had a major problem where my save file got corrupted and I almost bricked another cartridge for some reason. I got it back with my powersave dongle but I lost a lot of progress and a good three boxes of mons. I tried using Save Manager and SVDT both but each time I wrote the file I saved onto my SD card with PKHex, it keeps corrupting my game no matter which save (I have multiple back ups of the same save at different points in the game) I use so it looks like a PKHex problem. I still have my recent save but I'm currently unable to write it to my cartridge and the last save on my powersave, which I used to make my game playable again, was before I had any badges (I stopped using my powersave once I got OotHax). Do you have any ideas what could be causing this?