If she can get over it, the others can get in. You wouldn't want to leave the chicks anywhere that Mama was not around to protect them. IMO, either you should block hen and chicks in together, or leave them unblocked.
The concern I see with your set up as described is the 2 levels. If babies fall or get down to lower level, they may not be able to get back up. You might need to look at your set up in terms of the lack of mobility of a day old chick, and set up an environment that will ensure that they will...