I had that happen once. We were held up on a flight that was supposed to stop over and then continue on the same flight number. The company decided to put another aircraft on the second part of the journey, and luck would have it we both called in with the exactly same callsign in the same sector, one approaching, one departing. After a few initial seconds the controller simply told one of us we would henceforth be known as "mickey mouse" in his sector and that was sorted.