I am having the same problem with my broody hen! She gets up and stretches and while she's gone, someone else hops into her nest box and lays eggs. Then the broody gets all confused and starts setting on whatever eggs she can find. Some people put their broody hen in a different pen, with just her eggs (and food, water, bedding, etc) while she's setting. Then she can't get confused and no one else can lay in her nest. I left mine in with the flock and have had good results.
Always mark the eggs you want to hatch with a marker or pencil. I mark mine with a permanent marker. I put 2 big X's on, one on each end. This makes it quick and easy to determine which ones are the originals.
Mine chickens always seem to know exactly how long they can leave their eggs to eat, stretch, whatever before they need to get back to the nest. I wouldn't worry about her getting up, just check whenever you go in to make sure she's on the correct eggs. Plus with the warmer weather, the hatching eggs will stay warmer longer without mama hen.
Towards the end, the hens don't get up much at all. I always feel bad for her and take some treats to her box. I know this is probably unsanitary and might draw in critters but geez, she's got to eat, right?
Once the first chick hatched, I moved mama hen, the chick and the remaining eggs (and food, water, etc) to a dog crate in the hen house. I locked them in until all the eggs hatched and everyone was adjusted. I'd open the door when I was in there but mama didn't want to come out with the chicks until they were about 2 weeks old.
I haven't been raising chickens very long so I could be doing everything completely wrong but so far, it's worked for me.
Good luck!
