After running some tests it seems that the way to use the dynamic linking of assets across .blend files is to use groups. This allows huge changes to be made to the asset that gets updated in main file. This is what I wanted to achieve from the start and knew it was somehow possible as that was the touted workflow of Big Buck Bunny. The trick was that I was importing the object rather than having the object and armature grouped and linking to the group. This should allow me to start setting up scenes and animating with partially complete assets. Also another things that sucked an annoying amount of time is that both the armature and mesh need to have the centre-point moved to the world-space centre. This seems to be the way that you avoid the armature/rig disconnection issues that i have been grappling with.