I take it you didn't mark the eggs in case this happened. Then you know which to leave under the hen.
I have a broody Wyandotte Bantam that keeps sitting in the nest boxes and if I want to let her sit on eggs I would have to separate her from the rest of the hens as she goes from nest to nest after going out to eat. Another hen gets into the nest box to lay while she's out, when she goes back in, if the hen is still there she just gets into another nest box so the eggs end up unviable.
I have a broody Wyandotte Bantam that keeps sitting in the nest boxes and if I want to let her sit on eggs I would have to separate her from the rest of the hens as she goes from nest to nest after going out to eat. Another hen gets into the nest box to lay while she's out, when she goes back in, if the hen is still there she just gets into another nest box so the eggs end up unviable.