I have the same issue. I have a silkie, first time brooder, sitting on 5 eggs. She's in the one box out of 7 that they all choose to lay in.
It's about 3 feet off the ground, but has a high lip, so I think I'm going to leave her in there. We went out today and her sister was sitting with her, so maybe I'll have co-mommies.
I did mark the eggs she was on so I can pull the new ones out. She jumped off the nest when we did this, ate, drank, pooped and preened for about 5 minutes and then went back on the nest. I have high hopes for a hatch on 5/4/16!
I have 7 eggs in an incubator due in 6 days, so I ordered a second 'bator in case she stops sitting. If so, I'll grab the eggs and finish them in the 'bator.
Good luck with yours! Keep us posted.
I hope your hatch goes well too! At least if you're keeping your broody with the flock, you won't have integration issues later on. I'm hoping that re-integration won't be too bad for me, but this is a fairly low-ranking hen, so we'll see.
I'm supposed to get NPIP testing done for my flock in about two weeks, so hopefully this hen won't abandon her nest from the disturbance of being poked and prodded at that time. Like you, I do have an incubator that I can use as backup if I have to.