I repaired a corner of the slide-out roof in our 5er we had. The corner wood was "soft" and I cut away all that and replaced it with good wood, and repaired the roof part on top of it all. Eternabond and Dicor all over the place! :)
After the repair, it did not leak, but it was not quite right, because I created a high spot, and now a big puddle forms when it rains. Didn't like that puddle.
It might be better to leave the "soft spot" alone, and just repair the leak in the rubber roof. At least that way you will still have it level and not create a giant puddle that won't go away (until maybe it finds a way down--especially if it turns to ice and melts and ice and melts for a time)