A change in file structure and morph IDs caused scenes that used the version 2 morphs to break. Unfortunately, although it was posted in the discussion by some concerned users, this was only today brought to my attention.
There's not a clean way to fix this issue, so unfortunately there will be duplicates of the morphs. On the up side, they have different IDs so they shouldn't be confusing if you're searching in the Morphs tab.
The old morph IDs are located in Pose/Head/Expressions/AshAuryn
New morph IDs, plus the previously unreleased morphs, are located in AshAuryn/Legacy/Expressions