Clarifications

So after a long talk with the nurses and a doctor we got some better understanding of the situation. Ganglion cells develop from the top down as the baby develops. The first surgery showed that they were developed as far as the site of the atresia. The sample sent off from the second surgery was inconclusive because it was all scar tissue. Hence the biopsy so they can see if the cells extend all the way down or not. 

If they do, no problem. If they don't, it will require surgery which will most likely include a colostomy which means she would be pooping into a bag instead of the normal way until she is older and big enough to handle it being reattached. Here's hoping they rule this out.