I have a somewhat similar problem on my pop-up truck camper. I took it into my local RV repair place and basically the only option is to replace the whole roof, which is very expensive. As a "stop-gap", they gave me some awesome "tape" called something like "Emergency Repair Tape" (white on one side and has a thick layer of putty-like material on the other and is sold in 2' rolls) and recommended I seal the area with that and then seal the edges of that with caulk. This should keep out any further moisture.
Good luck!