She should be able to go back with the others now. Three hens is not enough to have with a rooster. They may suffer excessive feather loss from over-mating, especially with a younger rooster. Ten hens per rooster is a better ratio. Here is a good article to read about egg shell problems...
I would try giving her some extra calcium and vitamin D. Do you use layer feed and put out extra calcium in the form of crushed oyster shell or feed back their eggs shells to them? It sounds like she is not taking enough or has a problem with her shell gland. Probiotics are good for helping...