I have a broody in with the rest of my flock, and every morning I have to pick her up and remove the eggs that have just been laid (her original eggs are carefully & clearly marked in permanent marker on both sides). But I learned the hard way--with the same experience you are having!
It's true that the hen won't sit more than another day or two. I would wait and watch--when she gets up and leaves the nest, take the rest of the eggs in and candle them. If it were me, I'd discard any that were very early in development, but put them all in the incubator if you wish. But mark them according to your best guesses on development. If most are well-developed (mostly filling the egg and/or internally pipped), I would go ahead and raise the humidity in the incubator. You could even leave some in the turner and some on their sides, according to their state of development.
Then I would watch the eggs like crazy. As soon as each bird is most of the way out of the shell (even if it's still pushing the top off), I'd remove it to a temporary "recovery" brooder--a box with a towel in the bottom and a heat lamp adjusted to reach roughly 99-100 degrees. That will prevent accidents with the machinery of the turner. Alternately, you could just manually turn those that need turning, but then you'd have to be opening and closing the incubator and messing with humidity.
Of course, the higher humidity is going to mess with the eggs that are still early in incubation, and there's not much you can do about that except hope for the best and hatch them on their sides (as opposed to in cartons--I have a theory about this--I actually hatch in cartons most of the time but I believe that when air cells are underdeveloped from high humidity that eggs have better success hatching on their sides so the baby doesn't have to work against gravity to keep its bill in the air cell above the fluids).
Any way you cut it, unless you have two incubators, you're going to be messing around a lot to get the eggs to hatch. But I think you can pull it off if you want to.
If you *do* happen to have two incubators, then it's simple--prepare one for lockdown and one for regular incubation. Candle all the eggs, and put those that have filled the entire egg and/or have pipped internally into the hatcher, and the rest in the other. Candle every few days and move those that are ready into lockdown.
Good luck. And have fun.
