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Did the new unit come with flashing for the "top" side? I have some skylights that were professionally installed. They have different flashing kits to use, depending on which way the skylight is installed - long side up, or short side up.
I use geo-seal..its 100% silicone...dont use tar or roofing cement...it will only last a few years then crack.
If the skylight was roofed right the first time you would need any silicone at all...good luck....usualy to get a roofer to come out and fix that its starts at 300.00 and goes up....
If you have a new sub-divison around you go there and find a roofer that is working on a new const house...where is only 1 or 2 guy..these are usualy the roofers just starting there company...you can get a good roofer there for a cheaper price..
Good luck, if you have any more questions you can email me and I would be glad to help you
I dont come here too often so it might be better to email me if you have additional questions