That one is simply explained by her in DA2 if you bothered to listen to what she says.
Hawke first encounters Flemeth JUST after The Warden has left the Kocari Wilds with Alistair and Morrigan. She offers to assist in getting them to where they can get a boat to head to Kirkwall in exchange for him taking a vial containing a part of her essence on the grounds she figures Morrigan might want to do her over (naturally she doesn't tell Hawke this). So when Hawke gets to the point of taking the vial to the Dalish as part of the deal, by this point Morrigan may have got the Warden to 'kill' her and even if not the old 'vessel' most likely perishes when she is reborn via the ritual Merrill performs.
As for Leliana considering her limited conversation with Hawke, it'll be nice to get a proper conversation with her in DAI and so we can see the differences depending on the variables of her 'potential' encounter with the Warden (I say potential considering how you can avoid her almost completely in DAO). Maybe we will find out how she survived, maybe we won't. People need to just accept it and move on.
My god, I know that. That was aimed at the people that are surprised NOW that Leliana is alive.





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