According to The College of Arms, the authority for official flags for the UK and the Commonwealth, should the people of Scotland vote for independence there are no plans to change the Union Flag if Scotland becomes an independent state. They are quoted as saying that:
As the Queen would remain the head of state in an independent Scotland the Union Flag would not be affected.
Regardless of what the officials say it will be interesting to see what the public reaction would be should Scotland gain independence in September 2014.