I have a tragicomic problem, which arose after I joined the armature for eye animation with the armature for the head animation by Ctrl+J. Right after that the head becomes very small rotates 90 degrees and jumps into one of the eyes:)If I hide the head mesh, then the eyes become very big, move above head and overlap . I managed to partially solve the problem by unparenting meshes from the armatures, then joining the armatures by ctrl+j and then parenting back the eyes. It all worked OK, but I cant parent back the head, as it get deformed in a very strange way:)Any ideas how to solve this issue would be appreciated (beyond and above:))))))
I had a look at the file. This is caused by your shapekeys that uses vertex groups. Weighting is also assigning vertex groups. And that's what is conflicting here when you skin your headmesh. When i remove the vertex groups for the shapekeys before skinning then all works well.
So, first skin the head mesh, then create the shape keys for it.
After joining armatures bones matrices are rewritten relative to new armature and every child object or paint weighted object goes to its local coordinates. So the cleanest way is that first you remove any parenting or weight paint from joining armature and after joining redo skinning and parenting.