When you use a retrain token, and you hit the "Clear All" button, it clears your reputation traits that you pick out from Tier 1-4. But this is based only on the reputation that you have completed. Your exp points that you earn in that rep will still be there and will still be needed to verify that you cleared that rank. You cannot transfer your rep exp from one to another.
Also, it is good to point out that you can easily do both reputations simultaneously and are not mutually exclusive. You can be max tier in both Romulan and Omega rep and you can do both at the same time.