Nope, you have to unequip all your good armor, runes, etc. that you want to carry over before the final battle if you want to keep it. There's no opportunity afterwards to do so. It sucks, because that final boss is kind of rough, too.
I would at least equip the sun armor on someone in your final party, or spread it between them. It doesn't carry over anyway, so you'd lose it no matter what, and it's good stuff. I also brought some extra Flame Array Chain with me, since I had a thousand and it's not too shabby.