The whole idea of marking the eggs when you set them is so that you can remove any that are laid by other hens after they are set. That should be done on a daily basis if at all possible, otherwise the broody ends up with a nest full of eggs and sometimes she can't cover them all and the ones on the outside chill and that can lead to a less successful hatch as well as a staggered hatch.
Are you sure the broody is kicking them out or could it be that they are getting knocked out when the other hens are coming to lay in her nest. I would candle them to check viability, but if this is happening through the day when you are not there to replace them and the eggs are chilling, then even if they were developing, that could slow or stop development. This is why, in my opinion, it is best to give your broody a quiet, secure place to brood, where she can't be disturbed by other hens climbing onto her nest. I have an old cupboard with holes drilled in the door, that I keep in the hen house for this purpose. Once a hen goes broody, I make her a nice nest in the cupboard with the eggs I want her to hatch and transfer her onto that nest after dark and then close the door. I open the door once a day and encourage her to get off the nest and have a break for 10-15 mins and then ensure that she gets back onto the correct nest and shut her in again. I close the door whilst she is off so that other hens don't lay in it and open it again when she is ready to go back. She still spends a little time each day with the flock and raises the chicks within the flock, so there is no integration required but she has a nice secure nest to herself whilst incubating her eggs.
Usually when my hens start to go broody, they stop laying in the communal nest boxes and head off to make a secret nest somewhere where they can lay and then hatch their own eggs. If your hens are confined to a run and coop instead of free ranging, then they often don't have the option of making a secret nest and have to settle for a communal nest. I don't think it's really fair, if we want our broody hens to rear chicks, to make them do so in a communal nest when, given the choice, they would usually go somewhere dark and quiet and private. I like to give them that environment but in an accessible place of my choosing. There are then no worries about the chicks falling out after they hatch and being unable to get back.
If I was you, I would fit a demountable cover across the front of the nest she is brooding in so that eggs can't get thrown out and other hens can't lay in it and chicks can't fall out after they hatch. That said, chicks are pretty light weight and jump/fall quite some distance without getting hurt. The problem occurs when they fall out and can't get back and the broody is still hatching the last of her eggs and won't abandon them for the one that fell out. Finding an egg kicked out of the nest is one thing but finding a cold dead chick on the ground below the nest is really upsetting.
Good luck with your hatch. I'm on day 9 of my first brood of the season, so we may be hatching about the same time.. I've just candled them tonight. My little Frances was such a good girl, letting me check her eggs without any protest and carefully tucking them underneath her as I gave her them back. You have to love broody hens. They are priceless!...