I would clean the entire roof, scrape away all the dicor areas that are large, clean and scrape all the bubbles and all the peeling nearby. Then I would coat the entire roof top with a real good roof coating and then dicor the places where needed, (an eternabond the front cap seam which I have already done).
Most people recommend to get the type of roof coating made specific for RV roof's (such as what camping w sells). In any case, I have seen great results from others who have used Henry 887 Tropicool white roof coating. I used some to coat my skylight and I think I will do the entire RV rooftop with it soon, likely this year. Mine is still not too bad, just want to do it before putting some flex solar panels up there.
I think what happened to yours is moisture got under the bubble areas and the heat of the roof top at one time or another caused the bubbles due to the heat and moisture. When you start having pinholes anywhere, the moisture could present itself as an issue away from the pinholes and away from where the water first intruded. That is why I would clean it up and simply coat the entire rooftop at this time. ~CA
2010 GreyHawk 31SS