Parenting a linked mesh object to armature

So I have a file with just an armature and I want to link a mesh object from another file to use as the character mesh. I parented the proxy to the armature which worked just fine with regards to the skinning, but when I reopen the file the deformation is no longer in effect, and I would have to reparent to get it working again. Any ideas on why this is happening or if this is the wrong way to go about isolating the model from the armature?