When it comes to water leaking from the roof, after the joint at the front and rear cap, skylights are the “bad boys” when it comes to water damage. Couple that with the illogic of trying to seal leaks with layers of additional caulking and it is no wonder I spend a lot of time repairing the seal on skylights.
Let’s start from the beginning. First of all, when a skylight begins to leak, the leak will seldom be quelled by dumping on a couple tubes of caulking and there is not a chance it will be sealed using most of the types of caulking I see hanging around the perimeter of the skylight. Secondly, when skylights leak, they leak around the flange. They do not leak from the solid portion of the skylight base, so there is no need to caulk there!
To begin, the first step is removing the caulking around the flange and on top of the screws holding the base to the roof. This step is the most onerous and may take up to an hour per skylight depending on how much caulking has to be removed. Since you do not want to cut into the rubber roof and the caulking may be dried in place, this step most often involves the slow careful use of a knife blade. It is not necessary to remove the caulking beyond the base flange, as long as it is securely bonded to the roof.
Next remove the screws and carefully pry the base off the roof. Once it starts to come up, it is not too difficult. You should find a layer of tacky tape, also called putty tape, under the flange and it is the tacky tape that actually does the best job of sealing the base to the roof. As long as it is intact, the skylight normally will not leak, unless it has a break in it.
Clean off the tacky tape and the roof. It is not necessary to be perfect here, but you do not want anything remaining unless it is securely bonded to the roof. It is usually quite easy to remove all the tacky tape.
After you have all the old tacky tape removed, lay down a fresh layer around the perimeter of the hole over which the base will fit. Then screw the base back down using new #8 x 1″ screws. You can use pan head for hex head screws.
Once the base is securely screwed down, caulk completely around the base and over the heads of the screws using a caulk that is self-leveling and made for RV roofs. I use Dicor self-leveling caulk and find it works well consistently. Do not rush off to Lowes or Home Depot and buy silicone caulk. It will not adhere well and wastes your money! The caulk is called self-leveling because it flattens down and seeps into cracks and crannies.
After the repair is made, do not wash the roof for 24 hours to allow the caulking to set up and do not wash the roof with a high pressure washer that may loosen the caulking. When you are done, it should look something like this.