No one knows what the future will bring at the moment, the ink has barely settled on the transaction and there seems to have been no discussion about the intergration of the ex SkyWest pilots to Virgin. It may continue to operate totally separate, or may be like the old Ansett days where the entry level started as a Turboprop F/O and moved your way up from there. Point is no one knows, sky hasn't fallen in!
If it does you have a choice, except it or withdraw your application and wait for Qantas perhaps, or go to Jetstar. 2drive do you think the airlines care about the size of their hold file?