Flex rig additions that dont come in when linked

Hi i have created a charcter in flexrig but added extra clothing items. (hat, Glasses, Scarf)
I wanted the scarf to be animated later so have tried various ways of deforming the mesh…using bones, lattices and now hooks.

Now the problem is that all these ways work in the model blend file in varying scales of succession. But has i have already spent a long time on my animation i wanted the linked file to my model to just update in my animation file, which is what i understood the link property was for. But when i open my animation file the scarf is still un animatable but the hooks (for instance) are there but un editable. It must be something to do with the way flexrig importsd the linked file becasue it has the same problem no matter which way i deform the mesh.

Can anyone advise me of the proper way to ensure the deform properties (such as hooks) come over so i can use them.
I have asked several different forums including CG cookie but havent had much success and really want to get it sorted before i continue on with any more animation.

In Einsite i should have made sure the model was complete before i started animation but as a learner im definitely learning the wrong ways to do something.

Please please help It seems a small thing to sort but would make a massive difference to my animation if i could get it sorted.