Unfortunately there's not a lot you're going to be able to do without sanding out one or the other.  Polyester and epoxy just don't mix. 

Perhaps you could add a layer of onlay or something at that particular point to cover up the epoxy and then use the poly on that?

FrankP 

I don't understand why the polyester doesn't harden, the epoxy was dry and well cured, probably 2 weeks old before I overlaid the polyester. Will the same thing happen if I try putting a layer of polyester over any epoxy. I have used epoxy over polyester without problems before?

Bigfoot,

You're right, that is puzzling. I know that epoxy will stick to cured polyester but that polyester won't stick to cured epoxy. I've never heard of a failure mode where the polyester won't harden, though. It's always been that it hardens, then eventually  comes off (sometimes pretty soon after).

The only thing I can think of is that the specific brands of resins you used are incompatible without special treatment. Polyester resins work by mixing unsaturated polyesters with styrene. At normal room temperatures and pressures the 2 components just sit next to each other, but in the right conditions they start cross-linking and give off heat and excess styrene gas (which causes the infamous polyester stink). The catalyst is what starts the reaction going.

It sort of sounds as if something in your epoxy is either neutralizing the catalyst or maybe bonding with the styrene. The catalysts are usually organic peroxides, which form polyamides in the presence of amines. Epoxies can have unreacted amines, so maybe that's what's happening. If your brand and mix of epoxy has resulted in the presence of unreacted amines, the catalyst can be turning into a polyamide and losing its ability to catalyze the cross-linking reaction.

If that's the case, letting the epoxy cure completely and then thoroughly cleaning it (washing with water, sanding, washing again and wiping down with denatured alcohol) to get rid of the amines should fix your problem. But no guarantees, I'm not really a chemist. I just play one on the internet.

Good luck,

Laszlo