Hei Nina. It is not the heat of the epoxy polymerization that is a problem. It is the non-specific reactivity of epoxy compounds that can destroy fluorophores.
Epoxy compounds are very reactive and can form bonds with most surfaces. That is why epoxides are used in many glues.
Treat a control compound containing your fluorophores with the epoxy resin and see if they are destroyed.
I see that others have used HM20 or GMA etc, but I don't have so many options at the moment, so I will just have to try with a control and see what happens.