no, it won't be retroactive. If you are currently showing on the gw roster then I'd say leave it alone at this point. You should be good for this coming week. For last week's rewards you will need to ask Customer Service for compensation through the in-game Support system. Keep an eye on your ticket once it's open, and keep it open. You may need to go back and forth with them a couple times to get anywhere. Do you know if FE had already registered before you joined? If so, include that info in your communication w CS. Should help guide them down the correct path.
If you have any trouble or get nonsense responses from CS let us know. Good luck.