Hi Jeri,
I haven't come across this situation before but I did a little research. It looks like what you should do is only bill for one E&M visit for the day, but combine both visits to determine the code.
Per the CPT manual, "The most common practice is to report a single visit code per day, evaluating all services provided during that day to arrive at the correct level of service. Prolonged service codes may be used to report services beyond the usual."
So, combine the two services together, which may result in a higher level new pt visit or if the two services together were extensive, you may be able to use the prolonged service code(s).
For example if both visits combined warrant billing a 99215, or even the extended visit code, then you would bill one 99215 instead of a 99213 and a 99212. You can also bill for the after hours code.
Hope that is helpful.
Michele