Alternatively, considering Premonition seems to have Lucina's influence already, Premonition is a point that occurs in an earlier "loop" so to say. This isn't the first time Lucina's been back. --- I'm a Thinker, I could Break it Down. I'm a Shooter, Trust me Baby! As we jump out, feel it in the will! http://www.fanfiction.net/s/8572968/1/Project-Ignition
I would guess that Lissa had died by the time the children left through the portal, but Lucina didn't want to tell her so.
I think this makes the most sense. I mean, if you were from the future, and a younger version of a family member asked if she was still alive, would YOU say she was dead? If you consider the fact that Lucina described Future!Lissa almost exactly the same as Emmeryn, who Lissa has specifically said she wanted to be like, it sounds like Lucina is just telling Lissa what she wants to hear.