Hmm, definitely an issue. Maybe let her out, but put the chick(s) out too. Hopefully she will move around and poop, and then be ready to go back in (she will probably sit down on the chicks to keep them warm after a short time-- that would be the time to put her & the chicks back with the eggs.)
In that case, it's just a judgement call about when to move them-- moving might cause her to quit sitting on eggs and just focus on chicks, or it might not. Hopefully the rest of the eggs will hatch soon enough that it will not be a big deal.