You seem to be speaking about using acrylic paint on top of the Sculpey glaze. My first thoughts were "How 'small' is small?" And "How large is the whole piece?" But here are a few thoughts:
I suppose you wouldn't have much to lose by trying what you propose, although you should try it on the least noticeable and tiniest spot, or--better yet--make a few small tiles with the same materials to experiment on with fixes. Then you will know what will work. I once knew an old-style carpenter, who commented to me as he worked on our house (in another country) that one of the tests of a good builder is to be able to fix or cover up his mistakes, and in my adventures with polymer clay, I have found his words often come to mind!
You may find that when you put glaze over the place after fixing it, either the repainted spot may look somehow different from the rest of the acrylic paint, or that the new layer of Sculpey glaze that you have to apply over it does not blend in with the original one. Then you have to decide whether to live with it, or to try something more radical. With Varathane, I have often chosen the more radical path.
If the repainted spot itself does blend in, but the small new area of glaze looks "repainted," I would consider it worth re-glazing the whole sculpture right over both the fixed spots and the original glaze; that should solve the "repainted" look of the glaze. But I speak as someone who always uses Varathane on my clay pieces, sometimes multiple layers of it, and I don't know anything about the behavior of Sculpey glaze. Do people ever use two or three layers of that? When I have a problem such as you mention, I generally rub away the Varathane over the undesirable spot with a little isopropyl alcohol on a cotton swab (like the ones for babies), repaint, and then reapply varnish over the whole piece, but I don't make anything larger than, say, a rock purse or a covered tin. If your sculpture is very large, it may not be feasible for you to re-glaze the whole thing.
Anyway, start tiny and, if possible, unobtrusive, in case something doesn't go well. Here's hoping you get good results and that you will post about your final decision and how it works out!