Issue with subscription orders

Our Website sells books. It offers one-time orders and annual subscription orders. The one time orders are issued sequential order numbers when the purchase is made. The subscription orders are issued subscription order numbers when the purchase is made, but these numbers are not in perfect sequence – they skip, for example 335, 514 791, 875.
We are finding that when a one time order number is issued that is identical to an existing subscription order number, an unusual thing happens. The subscription order creates “subscription notes” (which are like “order notes”) using information from the non-subscription order with the same number. These subscription notes pertain to ship date, tracking number and/or order status. What is most troublesome is that many of these subscription notes are repeatedly emailed to the subscription customer. Recently, a subscription customer complained that he received 7 email notices that his order has shipped. We had to advise him to mark it as spam. Is there a fix?