I bet you $1.00 that it will be Nicole's baby that she lost. Think back - she never saw it, and neither did Brady. Baker told Brady the baby was lost, and then Brady went in and gave Nicole the news. I bet the Ej/Nicole baby is still alive and Baker sold it.
I think he felt guilty because of Nicole's reaction to the loss and that's why he helped her find a replacement (at first, until she turned into such a huge pain in the hiney for him)
Another twist - I think Baker knew it was a DiMera baby and possibly contacted Stephano. I think Stephano knows where the baby is (or worse, even has the baby stashed somewhere). That could be how he knew all along Nicole wasn't still pregnant and also how he found out about the baby switch. I think he sanctioned it in order to keep control of both DiMera babies and Baker was in his pocket all along. Could be wrong, but I can't wait to find out.
