I got the same issue also with pokemon lets go.... i also tried the latest version of pkhex, any suggestion??
i follow these steps
export the savegame with checkpoint
then move the msd in the computer,
copy the savegame to the pc,
open pk hex, add 1 ball, click on export main and save.
copy back the save game folder into the Msd - overwrite the old one,
then restart the switch, and restore the savegame (same name) in checkpoint.
It was working fine before the update to 1.1.1 and now also i got same issue on pokemon lets go as well, SD card erased and installed the new CFW atmosphere as well.
Thanks in advance