If you can, try posting your question here:
http://www.medhelp.org/forums/show/104
Doctors with lots of experience answer questions in that community, but there is a small fee associated.
I'm not a doctor, but I'd have to say the earlier the better on the amnio issue. With a skilled doctor (and it sounds like you are under the care of good docs) the pregnancy loss rate is low.
You may need the genetic information when it comes down to what care to provide when baby B is born. If there is a lethal genetic anomaly, it will certainly influence the direction of intervention towards providing only comfort care. If there is not a lethal anomaly, the doctors would need to know this to be sure your babies are delivered where there is excellent neonatal cardiac care available.
With twins, you have a higher chance of preterm labor, and knowing the genetics sooner rather than later may really help.
Good luck. What a difficult situation.