From about year 3 of my new 5er, the skylight was a constant source of
leaking. The ceiling fan hole and the shower skylight never leaked, but the big living room one did. I tried Eternabond and Dicor, neither of which stopped it.
I finally found
Heng's Rubber roof coating, which goes on like paint and gets in every possible hole. I finally got it stopped. I redo it every year.
Good luck with your skylight project!!
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"If I'm wearing long pants, I'm too far north" - 2oldman