You should be able to save when you have the forge loaded up. Hit the button and reload if it is not the enchant you want. Maybe not the speediest (or perhaps RP-iest) way to do things, but it should work eventually.
Actually, I just went to the Atronach Forge and upgraded my entire set of Ebony gear to Daedric, then upgraded my follower's gear for good measure. It comes out clean and unenchanted, ready for you to smith and enchant new powers on it. (You can definitely use gear you enchanted yourself for the upgrade, but when I tried using some Ebony Armor I had found already-enchanted in a chest, it wouldn't work.) Oddly, when I did the recipe with boots, it consumed the reagents and produced nothing -- looks like the boots recipe may be bugged (tried it with two different ebony boots, and across several save game reloads -- no luck.)
I'm glad I saved all those Dwemer Centurion Cores for decorating my house; I had 12 of them sitting around.