Just because the aircraft have been painted in Virgin colours doesn't mean JB will keep them. Some of VAA's 737's have been repainted and interiors upgraded and they will still be leaving the fleet within the next few years.
VAA pilots have been told on numerous occasions since the purchase of Skywest was announced that they (Skywest) have to many types and the company would like to reduce the number to 2 types. Another issue with the majority of Skywest fleet is age and that age is now dragging down the entire Virgin Australia fleet.