I doubt anything happened to her rather Boone's silence is part and parcel of Liz's absence. It could be there is some extraordinary situation that the show runners are staying quiet on like The Babylon 5 people stayed quiet on with Michael O'Hare but I don't expect it. I do think the writers are scrambling to come up with a way to bring Liz back for next season or just later in this one since the show revolves around Liz and Red. They wrote Liz into one hell of a hole. I wouldn't be surprised if they revealed this crazy Liz is the imposter and the real one is revealed to have been in hiding since the wedding and 'death' way back when or even as far back as escaping the Russian embassy as Masha Rostova.