I have a mesh with 2 eyes parented to the head bone. Their rig is one bone that they track using a Track To constraint. When I export to .fbx and re-import the .fbx to Blender the following problems appear:
The eyes unparent from the bone, get teleported in a weird position behind the character and their constraint disappears.
The rig adds a "[bone name]_end" to the end of every bone that doesn't have both tips connected to something. Also, some of my bones, like the deform ones disappear.
When I export, I select "mesh" and "armature" and don't bake the animation, because I just need the rigged model for Unity.