Can anyone offer some help on this?

I really don't know the answer as to why it would work that way,  but you might try copying the repeating order to a new repeating order.  It wouldn't surprise me if it dropped the credit card when doing that.  No guarantees.

Is the repeating order that big that starting from scratch is that time consuming?

I'm assuming you a referring to the repeating order not the standard order created from it.   Changing it on the standard order could be problematic if the authorization has already been processed.

The credit card info in a repeating sales order isn't particularly useful.  It was the customer's default credit card at the time the repeating order was created.  There is no authorization in a repeating order.  When a standard order is created from a repearting order, the customer's current default credit card will be used.

You need to change the customer's default credit card or select a different card in the standard sales order.