What I do is run atmosphere for 9.1.0 and change over to customer firmware. Then I'll run a backup in Checkpoint and then use FTPD to transfer the save to my PC and use PkHex to make changes. Finally I run Checkpoint again and Restore the changes to my Switch save. I open up Sword/Shield and double check everything took effect, Once I know that my changes are in game, then I'm done. I turn my Switch off. Not asleep, not a restart, OFF. While it's off I put back all my stuff I needed to run atmosphere (USB-C cable, jig, etc). Then I turn it back on, I go to Settings and double check I'm back on stock firmware 9.1.0. Then I'm safe to get into the game and go online. Hope that helps.