Your question should be directed at the contractor. But IMO if the skylight is not leaking, I would not mess with the flashing.

IMO the solar needs to be where the skylight is I would not bother with the skylight after the solar is done. I guess I need more info as to why the solar needs some different roof and I think redoing the roof is maybe removing all the old before the new might somehow impact the skylight .

Probably remove them to reflash them. Are they a curb or a step flashed skylight?

If the roofing around the skylights is being replaced, there is no way not to disturb it. The shingles tie into the flashing, it really can't not be "messed with". "R&R" could really be referring to the flashing kit aspect, but also once you are at that point checking the overall condition of the unit is easy.

The real question is why designers would comment on the technical aspects of this? Geez louise Bev and Pat. No wonder you have 43k and 84k comments. Congrats on the ultimate in high volume, low quality.

Thanks, they're Velux step up skylights. Background is the roof is a 50 year life variety, installed 2009 so 14 years old now. There are some vent caps that need replacing and a new boot on the soil stack. Asked a company about their replacement and got back an estimate to repair/replace those, plus reroofing the section where solar panels would go, and removing and resetting the skylights. With a note about them not being covered for interior damage to skylight shaft. That note is what made me think they are not just redoing the flashing/shingle portion but as they said removing/taking off the skylight. Of course present flashing/shingles would be taken off and the new go on. Just don't see the point of removing them entirely unless they're found to be not structurally sound, or damaged in some way.