Flemeth's 1st appearance in DA2 would have been after she saved the Warden at Ostagar, but before you see her again for Morrigan's companion quest, so she would have had to change into her new appearance, then back into her older appearance, then back again into her new appearance.
As for how she was inside the amulet, I assume she just used magic to put a part of her inside the amulet because she was assuming she was going to get killed by Morrigan. Why you had to go to the Dalish and release her, she hints at the fact that someone/thing was watching her and she was unable to move freely. No other mention of Flemeth or what could possibly be a danger to her is made in the game, however there were a few hints (both made by Sandel) of some super crazy magic shit going down soon, and an old lady with a crazy laugh staring at Sandel as he lays in bed.