supposed to be flashed to the roof, then membrane or felt, flashed again so that the first flash is under the next flash going up the roof...all joints are running down hill so any water flows over the next one down hill towards the gutter or roof edge. Once all that is properly done, then shingle as close to the skylight but NOT nailing through the previous installed flashing.
Given the new roof, I would be searching for the company that did it, or at least asking the realtors to get involved for that company to provide warranty work if at all possible.
Going forward, explain to her the fewer holes in the roof the better. And if she buys another house, to get all of the recent paperwork about things like HVAC, shingles, etc. OR adjust the purchase price and do all this on her watch.
Many times sellers have the cheapest work possible done for the sale.