It’s going to be a convoluted reason that doesn’t make any sense. The actors chose to leave, so the writers had no choice but to scramble for any explanation whatsoever. I wish the writers could have been brave enough to let Emma sacrifice herself in the S6 finale rather than bring her back to life. It would have been sad but knowing that JMo would leave, but it would make the most sense and would have been true to the savior/mother character we knew in S1-3. Now fans will always wonder why she isn’t there to help Henry. Having a second child is not a handicap and shouldn’t prevent her from being the savior. The real Emma Swan (before she began acting totally OOC) would never have willingly forsaken Henry, no matter how grown up he is.
"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy