It's hard to decide whether Ian will choose Sally or Amy to be restored.
In the latest Sonic Universe when Amy and Cream return home, Amy mentions that things seem a bit off. So maybe she still has her old memories, otherwise she would think things appeared normal like Tails did before his memory was restored. Therefore, they wouldn't need to use Nicole on her.
However, if that's not the case, then Ian will have to choose Amy simply for priority reasons. She's a SEGA character, so she has to have the first dibs on stuff like this. Otherwise, if he chose Sally over Amy, then things just wouldn't seem right in the story.
Plus, with the new reality, Ian might be getting rid of Elias and Alicia. So if he were restore Sally's memory of the old world, then she would remember them, and a whole new situation would arise.
I still hope Sally gets her memory back somehow. I don't want her to forget her old feelings for Sonic, especially since they JUST STARTED going out again!