To be fair Neal never knew Emma was pregnant because she found out when she was in prison and he was out of her life by then.. I felt so bad for Neal because it was August who kicked him out! He truley loved her 🙁
I guess my theory was wrong about Neal and Emma, but I still hope he is Baelfire through.
I had a suspicion that she was pulling the fake pregnancy scam interesting she found out she was pregnant while in the pen, also it seems as though that story she told Henry was 100% made up lol