When I had a skylight leak, I had to look carefully but I spotted some hairline cracks in the outer layer (mine had an outer and inner plastic). I used 2" Eternabond on those cracks (and it hardly affected the light that made it inside) and 4" Eternabond around the edge of the skylight where it joined the roof. I scraped and cleaned up much of the old self leveling caulking before laying the Ebond.
Here's how it looked before I noticed the cracks in the dome...
Years later, no leak, but it did develop another crack as the dome aged out. Sealed that crack with Ebond too.