I was unaware that entities of the same type with the same animations could not be batched, so we put them in a batch group. The entity moves and animates fine, until something in the scene graph is edited (add, remove, disabled). Then the entity removes all animations and reverts to a mesh-only state.

Removing the animated entity from batch group allows everything to work fine.

Here's an example:
https://playcanvas.com/editor/project/1471010