I'm very near having to do the same. Mine is not leaking at all, never did as far as I can tell. It seems my 1/8" Luan skin is buckled upward. It has gotten wet from interior condensation under the rubber roof ( most of my camping is cold weather with lots of interior heat). Also I keep an Adco cover on TT?? When not using it This may have been a mistake, not breathing.
I don't think you can easily remove the Luan skin from the foam. The joists are there, just be careful on foot placement.
For that reason I would remove the damaged Luan if you can, and re skin entire roof with 1/8" Luan again, prior to new rubber roof.
If you use 1/2" this will adversely effect the edges, and the AC unit on the roof will be raised along with the skylights.
There are several you tube videos I have watched, in preparing myself for the dreaded task. BTY mine is 2004 FR Flagstaff 26SS
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