Instead of deleting all physics bodies, I found that aligning them properly did the trick.
This flickering occurred for me when I there was scaling involved in the mesh animation, and the physics bodies were not the correct size.
Turning up the higher bounds will work… however: the bounds determine when an object should stop being rendered while off screen (aka culling). If that bounds is too big, it will always be visible, but may cause a heavier strain on your graphics performance, especially if you have many objects with high bounds.