Linking aritfacts after reloading and relocating

I am having some issues during linking. I have prepared my file by hidding (unchecking eye icon/render viewport icon etc.) all the neccessary stuff and putting everything in one group. After I link the file and reload/relocate to update the rig, sometime black unselectable controls appears in the viewport. Is there a way to clean the rig file like deleting unused contraints or bone, something like that?
Thanks :slight_smile: