I have had success with this kind of problem using the highly liquid silicone windshield sealant (Permatext or similar brand). It flows into gaps in the silicone bedding and has worked effectively on portlights on a couple of occasions when the time and location of a leak were not suitable for a complete r and r. I sailed from northern Washington state to La Paz in Mexico with this repair in place on a forward cabin port light that took lots of water from some at times big seas. Mask off both sides of the suspected area along the skylight and apply the liquid silicone between the strips of tape. Use whatever method you normally use to remove the tape when you are confident that the silicone has suitably dried. It has been four years since the above repair was made and it seems to be still working fine.
On a larger port light in the salon, I have had to apply this fix a couple of times. I intend to replace the lexan so have been delaying a more permanent fix.
good luck
Nello
S/V Marathon
