Leaky skylight with foam roof

We have several skylights in our Eichler (flat foam roof installed
2003). One of them has started to leak a little (just a little, twice
in the past couple of months - once yesterday, and once a couple of
months ago (yes, there has been plenty of rain in between, whre there
was no leaking)). I took a look and didn't see anything obvious...

If the recommendation is to get a new skylight (as opposed to
repairing the old one), will this interfere with the foam roof? It
looks like some of the roofing material (not sure if it's the actual
foam roof material or the coating (we had it recoated last year))
comes in contact with the metal frame of the skylight. So if the
skylight is replaced, would that "break the seal" of the roof (or
damage it in some other way)?

thanks
Eddie
Palo Alto