I had this happen a few years ago. Wifey and I had an Open Jaw EWR-MSY/SEA-EWR in May 2014. On 30-Dec-13 I got a mysterious refund on my card for the full amount of the ticket. Then on 03-Jan-14 I got re-charged the same amount.

In your case, it sounds like the excess refund is linked to the cancelled trip, not the new one.

The best advice I can give you is to be prepared to pay that amount back at boarding. Keep your paperwork (original ticket receipt and credit card statement) to prove how much they accidentally refunded you in case they try to get you to buy a new ticket last minute. You could even check your itinerary one every other week and make sure it doesn't show a balance due.