Yes this is pain

Same applies with the gui being pulled up through command and I personally think the best way to fix this is to either dump the contents out into the players inventory or out onto the ground before clearing the inventory tags the Shulk uses. Id argue keeping the tag on every player but because this is a creative item that can be attained through recipe data packs. Its recommended to dump it out because then players use more resources to get it back if its stuck there if there using that method...