Below is what our roofing expert John Stout from
Go Roof Tune Up had to say in response to the question:
You are on the right track. A roofers reputation is highly valued. We all work hard to establish and maintain a good reputation. We do not know exactly what the condition of your roof is. We assume it is asphalt shingles. You mentioned that your old roof was asphalt and was not nailed down. It can be assumed that it was not ”properly” nailed down. With the new shingle roof installed it is now properly nailed. The common sheathing material prior to the 1970’s was 1X6. Now it is rarely used for sheathing for various reasons. However, it is adequate and not necessary to replace. Often times when a shingle roof is removed, some damage will be discovered; it is necessary to replace if substantial. Small holes can be repaired with sheet metal or asphalt impregnated rigid insulation. Your description points to the holes being covered with insulation and then roofed over with shingles. That would explain the shingles sticking up. If the shingles are unsightly, it may be that the shingle could be removed. Then you can replace the patch with metal and shingle over it. This should solve any aesthetics issue and would not affect the warranty.
To comment on your final thought, no it is not necessary to re-sheath the roof to install new shingles. We thank you so much for contacting AskARoofer. We are convinced that the majority of roofers in the area are reputable and will bend over backwards to have a satisfied customer. That is how they get their next job.
We thank you sincerely,
Your friends at AskARoofer