The best option would be to remove the roofing up to the ridge, because that provides the best likelihood of keeping the waterproofing intact.

Thank you-- does that mean remove rafters and all??? That is our concern

Not necessarily. In California, we do a thing they call 'California roofing' (not sure what it is called elsewhere) where the new roof structure is built over the existing. It can require some work in the framing but that would be determined by a structural engineer. It is done all the time. Whether it is an option for you would depend on the specifics of your project.

You would generally put a continuous 2 x 12 flat on top of the roof and frame new rafters on top of that. It is essentially the same thing as framing in a valley on any other roof you see. You should definitely have a structural engineer look at it first.