In your App I would suggest designating one of the shops in the group as the ‘Billing’ shop. This is the one that has the non zero charge associated with it.
Your shop listings page could have a feature to allow the merchant to change which shop is the Billing shop. To implement this you would delete the existing approved recurring charge and create a new charge for the other shop. The merchant would then need to login to the other shop and approve the new charge.
Your app would need to handle the state when there is no shop in the group designated as the Billing shop, such as when the transition to a new shop is happening, or when the previous billing shop uninstalled the App. I would suggest that in this state you simply redirect to the shops listing page saying you are waiting for approval from the new shop (if they are transitioning), or they need to choose their new Billing shop if there is no approval pending.
HTH, Gavin.