Gypsy –
The way I understood it was that the water restored what was taken away including (I guess?) restoring Emma. It seemed weird to me too (I guess I need to look at the wording from King George about what the potion was capable of – preventing any future pregnancies or cancelling out in progress ones as well – though his knowledge could be limited as well) but in that clip from the end of the episode Snow was upset and about to have to tell Charming they couldn’t have the family he wanted. She almost refused the necklace and then it started swinging which means that she was pregnant at the time. It didn’t move before when Ruth tried to give it to her because it was after the potion but before she drank the water.
Not sure the extent of the powers of water from Lake Nostos but that was my understanding of the episode. It explains Snow’s change of being upset and not wanting the necklace to being at peace and knowing things were alright even though it does seem very strange. As I said before it was very subtle but she does put her hands on her stomach after Charming throws the sword at the Evil Queen in the pilot.
I doubt much time has passed between the 1st wedding and the 2nd, but it definitely appears that she was pregnant in Lady of the Lake since the necklace worked at the end (after she drank the water). Perhaps it has something to do with Emma having magic? (Besides being the product of true love, she’s kinda a miracle baby if this is what they meant to imply with Snow drinking the water and the necklace working immediately after that but not before).
Keeper of Hook's Trenchcoat.