"virtually all skylights are installed at the factory with butyl tape underneath and dicor on the outside. Dicor is one of the few sealants that will stick to EPDM roofs. and this system seems to work for a long long time on skylights.
I know some skylight mfg recomend a different sealant underneath and on top, but personally after replacing one I would NEVER use anything other then butyl tape underneath. It is reasonably easy to break the seal for removal with butyl tape and dicor. other adhesives under the skylight are going to be a REAL problem to break the seal to replace the skylight without damaging the roof."
Yes, I used butyl tape under the skylight. I think, but am not positive, that my original skylight was acrylic which is compatible with Dicor. The replacement is polycarbonate, a tougher material, but not compatible with Dicor, thus the need for butyl caulk.