The Pet Zapper works fine but after doing his work, the tokens are still in my inventory. I just zapped my pet Flamethrower from Arid Keeto to Field Ruffie and the 15 tokens were not picked. I'm on Chrome.

the tokens for zapping are taken from your currencies rather than your inventory (you can add them to the currencies by clicking the option from the inventory)

Thank you for letting me know! That explains everything :D