My '97 Hunter Passage 42 has a very large skylight on the forward facing part of the main cabin - covers most of the width. One corner had loosened enough to leak during rains - was not noticeable when washing the deck; likely not enough water. However, it was enough to require a re-bed. Especially needed as I am now cruising outside the US in a place where there can be lots of heavy rain.
For the sealant I used used Dow 795, AS RECOMMENDED BY Hunter. To remove things I attached suction cups and applied slight tension using halyards (be sure to use a "safety" to cord to prevent the possibility of anything getting away <Grin>). From the outside, cut into any sealant than can be accessed. After that, slide very thin metal scrapers through the sealant from the inside and cut away the remainder of the sealant. As things start to loosen the lifting action of the cups make it easier to get to and cut the old sealant.
Next, of course, is the obligatory advice to clean everything thoroughly several times. Use LOTS of the sealant so it can push out all around to assure a good, and complete, seal. Tape all nearby areas of both fiberglass and the window to keep them free of the excess sealant - makes cleanup ever so much easier <G>
BTW, the suction cups are also likely to be useful when reassembling...