There is a simple device used in helicopter rotor blades that might work. It is called a leading edge strip and is used on composite blades to prevent leading edge erosion near the root, edge strips nearer the tip are made of stainless steel but at the root it is only a strip of vinyl for protection. It works well there because the air flow is not as high as near the tip. Aerospatiale blades use this type of protection on their 350's.
To apply the vinyl you use Methyl Ethyl Ketone (MEK) as a solvent to soften and make the vinyl sticky and then apply to your paint. Sticks like mad so you have to work it a section at a time but it works great and prevents water infiltration from causing corrosion. You could cut up old water bed bladders for the liner, they are virgin soft vinyl. I have used this technique for protecting fiberglass boat bottoms from keel scratches when landing on a beach or on rocks, I use a heavy gauge vinyl in this type of application.
To remove just use a heat gun on low and a rigid plastic spatula to strip off the majority and then a rag soaked in MEK to remove the residue, voilá you have perfectly virgin paint underneath with no corrosion due to the water tight bond.
I have never done a surface as large as a roof but have done many boat keels this way and the water never gets underneath even on aluminum hulls. Since you don't need a real heavy gauge vinyl on the roof it should be easy since you can stretch it to remove the wrinkles. Might be worth a try on a keeper? Just remember to work slowly and not use too much MEK, just enough to make the vinyl tacky.
Little tip on MEK (methyl Ethyl Ketone) it will clean anyuthing off of anywhere, its awsome stuff, its very very flamable and can eat through anything and it will give you that costly chemical peal that rich oold ladies pay $5000 for at a spa, hehe, but just be carful with it, DEHEC told our shop we had to quit using it, they say its very bad for you, good of them to tell me after I've been using it foir 5 yrs, hehe
MEK is safe to use on all paints except for laquer. It has similar properties to alcohol and evaporates at nearly the same rate, make sure you use plenty of ventilation and wear rubber gloves. I used the stuff at one place in huge vats to remove laquer paint from Bell 204/206 blades, I was not too pleased to hear that it was labelled a carcinogenic later either. We used to be up to our elbows in the stuff with the ony immediate side effect being dry skin, of course I know better now.