It seems clear there are plenty here who would prefer to sit on either side of the fence.
In this case specifically, looking at those pictures, do you really think there is going to be a problem with leaving that felt on? Seriously? Is the roof going to fail because of the extra felt? Is it going to leak because of the extra felt? If there is a hole in the roof under those new shingles
big enough to warrant worry the OP would have noticed, and we could have a much more serious point of contention to be debating here.
The only thing I see is two layers of felt...no major warpings or dints in the newly applied shingles or felt to tell me there is a giant hole in the roof. With the mention of wind damage I would be a lot more concerned with the shingles staying on than an extra layer of felt.
With the old shiplap if there was a relatively small hole we would
and still will just slam a flattened piece of step over it rather than go to the lumber yard for that perfectly matching piece of shiplap to cut in and replace a 6"x6" hole. That flattened piece of step is going to save the homeowner coin and its going to save the roofer the headache. I dont care what you markup a square foot of sheeting for profit, it's never going to be worth it to replace it when you can metalize it in 5 seconds flat for the same desired effect. Of course it's going to fail inspection but it sure as hell isn't going to leak or cause the shingles to fail prematurely

. And if the roof caves in because that piece of step flashing wasn't strong enough, it's either because you just got 20 feet of snow overnight or pterodactyls are no longer extinct and are roosting on your roof (apparently they were a lot bigger/heavier than your average sparrow for example)...
Now when the hole gets bigger than a piece of flattened out piece of step, I say fix it with wood, and do it right :thumbsup:.
Honestly, structurally speaking my biggest issue is with lack of support around vent holes. I broke three ribs once when an area of sheeting around a poorly supported vent hole collapsed and my ribs saved fme from fixing the drywall inside. Yet how many guys go inside and frame-in vent holes? Haven't seen it yet let alone hear of it.
FTR I fail to see what Mexico has to do with this.
There comes a point where discussions get ridiculous, and this one is getting there. How about we close this and move on.