At Crytek, we have a plugin to preserve skinning on hacking up and uniting meshes, based on this old post here. It’s released in the Tools folder of CryENGINE if you grabbed the engine on Steam. Imagine my surprise when I saw this option in Maya 2015:
It fires off a new polyUnite command called polyUniteSkinned [Maya 2015 Docs], which can merge skinned meshes? Has anyone gotten this to work? It doesn’t seem to work properly through the UI, passes ‘name’ as a flag and fails as they removed that flag. (seriously) But it seems to work in simple situations, as shown here, it didn’t work attaching a face to a body, but at least it shows ADSK is moving in the right direction!