Hi -
First, I am so sorry to hear about your loss.
Second, YES! You can definitely have a baby while having an ovarian cyst. I went to the ER at 6 weeks for pain (the doctor was concerned it could be an ectopic pregnancy) so I had an ultrasound and it revealed I had a 6cm ovarian cyst. It was later deemed to be "para-ovarian" (just means it was next to the ovary, not *on* it) but still - I was able to go to a full 41 weeks before delivery a healthy baby boy.
Now had they known I had a 6cm cyst before I got pregnant I believe they would have suggested removal. I was monitored more frequently by ultrasound during the pregnancy but it never was an issue. I also have heard of people who have a typically successful surgery between 14-16 weeks of pregnancy to remove large cysts if they become a threat.
Bottom line - yes, you can have children despite having ovarian cysts. (Let me qualify that by saying I don't know anything about endometriosis - I know that can inhibit pregnancy - but in general the cyst itself does not mean pregnancy cannot occur.)
Hope that helps.
Cysts are very, very common. Smaller ones can come and go and be completely unnoticed causing no noticeable symptoms or problems. It gets more complicated as they get bigger, complex or solid.
There must be some medical explanation for the loss of your pregnancy (my sincere condolences!) but someone with an expertise in this area needs to help with your question.