Can a damaged roof rafter be replaced without removing roof decking and shingles?

Cut a new one to fit and slide it in next to the old one. Nail it the best you can to top plate, ridge board and the old rafter.

If the whole rafter is rotted do what magprob said. Your going to "sister" the rafter.

If only a small area of the rafter is rotted & not split you only need to span the rot by about 2' in either direction on both sides of the rafter. 3/4" plywood works well for this.

As for the roofing contractor, most guys don't inspect the attic unless they suspect something is wrong when they are working on it.

If he did and the roof leaks after 7 years, I doubt he'll do anything about it. Guarantee is over. He would only guarantee his workmanship and not material defects, storm damage, etc. There could be a number of factors to why the roof would possibly leak.

If the roof is now leaking you should see signs of it on the attic insulation and the ceiling below.

To answer that if a new roof was put on, no they don't inspect unless you tell them to and give you a est to fit it completely. Most people ask what it would cost for another layer of shingles to be put on their roof,

Next it may not have been bad 7 years ago.

My main concern is how good is the plywood or other material if the rafter is bad, have you tested the actual roof to see if it is bad also..