If a payment is made against a booking incorrectly, you can easily move the payment from one booking to another (it needs to be of the same booking type). To do this click into the booking that has the payment associated with it, from the left hand menu click on the Admin link.
From the Stripe Payments panel under the Reassign option enter in the booking reference that you wish to move the Stripe Payment(s) to, once you enter the reference click on the 'Move Payment' button to complete the swap.
Note: Only paid records can be transferred, payment requests cannot be moved.