i think Baelfire was turned into ageless object or animal until he came in contact with Emma. i prefer a frog but anything will do.
What if it was the reverse? Emma finds out she’s pregnant and – poof- Bae is turned into a frog. She can’t find him so it looks like he has run off.
Since Mr Gold/Rump poured the potion into the well, the water touches many lands (can’t remember exact words) maybe the water will come in contact with Bae in some form- human or ???. Maybe this will draw Bae back to SB or send a signal to Mr Gold so he can go to Bae’s location.