Is "she" the baby or "she" the niece?
As far as I know the fact that she, your niece, is having a miscarriage has nothing to do with her having cf. What symptoms was she displaying that led to a cf diagnosis? As part of her prenatal blood workup they might have screened her for the cf gene and found 2 copies meaning she would have cf. It's a double recessive genetic disease like sickle cell or tay-sachs is. It is unlikely that they would not have mentioned it as soon as they found out this news but maybe her emergency situation brought attention to her file that they'd neglected before??? Sounds like there's some missing information here.
In answer to your question it doesn't really effect pregnancy except that mother's have a tendency to deliver babies with lower birth weights. They also tend to deliver between 35-37 weeks. Mothers might have more difficulty breathing depending on their lung function going into the pregnancy. I've never heard anything about an increase in miscarriages and as you can see I'm pregnant. I did a lot of research before getting pregnant too. What it does effect is the ability to conceive, men have CBAVD (missing or severed vas deferenes so the sperm is in there but can't get out) and women have thick cervical mucus sometimes inhibiting fertilization.
Does your niece have any of the following: frequent chest colds, sinus problems, inability to keep weight on, decreased lung function for no explainable reason, taste salty? These are all signs of cf.
If they did genetic testing during routine blood work she might very well have a diagnosis. I really think they would have mentioned this though because they would have wanted the father to be tested so they could determine the risk factor for the baby having cf.