N.B.
Hi H.,
First of all, I think you need to know that everything is going to be all right! It sounds as though you are an excellent "baby maker" having had an exceptionally healthy baby girl as an example. As long as your son has an artery and a vein in the umbilical cord, he can exchange blood normally and that's really the biggest concern.
When we had our little boy, my hormone levels were elevated and they said that I was going to have a Down's Syndrome baby because of it. I completely stressed about this for the entire time that I had to wait in order to have a level 2 ultrasound (several weeks) because my husband had absolutely NO interest in having a special needs child and I knew I'd essentially be a single parent, if it didn't end my marriage. Everything was fine though. I think I cried with relief when I saw his little profile and the nurse commented on his "big nose" (Down's babies generally have no vomer... bridge to their nose).
What they DIDN'T tell me right away was that there was a 97% chance that my baby would be fine and only a 3% chance that he'd have Down's. I'm sure it is the same type of situation with you. They feel that they have to tell you that there is a chance of low chromosome count and heart defect, but there is a chance of that even with three vessels. There may not be much difference in the "chance".
Everything seems more magnified when you're pregnant and I can remember only too well the stress I was feeling during my first trimester with my husband not wanting to be a father (he's an EXCELLENT dad), the tri-test results, waiting for the level 2 ultrasound... it sucked to put it mildly. Most of the stress was un-necessary... and I think that if you can focus on the positives, everyone will be healthier and happier throughout. I know it's hard, but hang in there and try to relax and enjoy your second pregnancy!