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The source of your trouble lies in the fact that there area couple of studies indicating that when htere is no way for heat in the roof to disperse on the back side, the average temp of the shingles is 2-3° higher. Hotter temps cause a faster off-gassing of volatile oils so shingles dry out or age faster. How much faster is still an open question. The studies that show the worst problem are where shingles are applied over a foam insulation and or radiant foil that redirects heat to the back side of the shingles. Not all manufacturers have indicated that they void warrantees due to unvented attics. In many places with cathedral ceilings or denspack cellulose insulation, venting is not called for.
The sum total of all this is, I wouldn't worry about it. You may not have a valid warrantee from Elk for all manner of failure but you have good shingles and probably a good system. removing the insulation is not a cost effective option, IMO unless there are other indications of problems with condensation or something else.
It's kinda like paint or coatings. My friend has a log cabin house. Sealed with Behr's coating. The beautiful red cedar color is turning black. Behr's says they'll replace the coating $1000. Big deal, it's going to cost $12,000 to blast off the old crap with walnuts shells. Do they really think he would put that crap back on his house again? I think not.
You are in same boat. So they replace the shingles, so what, they won't pay the roofer to tear em off and put the new ones back on. Don't too worked up about the warranty.
I am assuming the roofer is tearing off the roof deck and installing new? Sounds like the attic is accessible and if it is I would hire someone else or do it myself as far as the insulation. Otherwise bite the bullet and pay him.