My name is Jade, I am with the Support Team at Shopify!
The iPad identifies the cash register through the receipt printer. The receipt printer can only be paired to one iPad at a time. What will happen is once you pair the second receipt printer to the second iPad, it will automatically connect to the correct cash register, which is your new cash register because it is not already connected to a device.
I hope that makes sense! Let us know if you have any questions!