I have a character that switches from armature control to a rag doll controlled by the physics system using bone constraints. It works fine when playing in the viewport or when rendering a single frame, but does not work when rendering the whole animation.
I found this article that seemed to have the same issues. The response was:
"This is a known issue in our current depsgraph, there is a workaround for it though - enable Extra Object Update and/or Extra Data Update for armature and ant mesh, in Object buttons, Relations Extra panel.
Anyway, not a bug, rather a known TODO for our future new depsgraph. ;)"
But I don't see those options in 2.8. Anyone have any suggestions?