Hilariously, the master ball was not deleted from your inventory, and the commands to delete thrown master balls possibly would not have worked because they didn't center on the player.

I'm a little confused where the quest book runs commands from, and a little concerned that the execute at @p is not going to work when there is more than one person in the world.

I added
execute at @p run clear @p poke_ball

I also put an execute at on the other commands, which didn't seem to be running.

Tester declared it fixed.