I'm not sure about the money to be paid out if the 1st layer is replaced, but once you get a quote and send it to them, they will give you the depreciation back. I just went through all of this with SF.
Thanks! I have SF too, I didn't know that's how they approach it. Mind telling me what contractor you went with? The two biggies in my subdivision so far are Dula and Integrity, but I trust all these guys as far as I can throw them.
As for leaving the first layer - no way. As it is, there is some staining on some of the plywood visible from the interior due to the shitty job they did putting on the original roof, coupled with nail pops. I want them repairing those areas. They also left inadequate overhang in various spots, which would look like crap if just gone over.