On version 2020, the most current update, I am unable to make this happen on a NEW customer.  It should only prompt you if the customer has existing repetitive invoices if the original value is on the repetitive invoices.  You cannot enter a repetitive invoice before the customer is created.  Is it possible you are on a lower version, there are 3rd party modifications or if you can duplicate on version 2020, please send the exact settings and steps to duplicate the issue.

I am able to duplicate this on version 2020.  After creating a new customer and entering a new contact followed by a ship code I get the prompt - Do you want to update repetitive invoices.  If you just enter a new contact and no ship code you don't get the prompt.  If you just enter the ship code you don't get the prompt.  

If you enter the customer and new contact, then save the record and go back and add the ship code you get the prompt also.  If you change the ship code on an existing customer you get the prompt even if there are no repetitive invoices.  

This issue will be fixed in 2020 PU1 and 2021.