My ‘companion’ is lost. I had him, he died, I revived him, re-installed armor. But, he does not travel with me (which makes it really hard to get schematic points) and his name is gone. He’s there where I rebuilt him, but he stays there no matter what. I tried to make a new one but I guess you can’t while you still have one. I can’t pick him up or interact at all. This just started a couple of days ago. I was in the Beta, so I went back to the regular game and it’s happening there too.
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I also lost mine when transferring it to the Plundra box
My deepest thoughts with your loss 
Already tried to process it via the companion station, e.g. Weapon swapped or armor? For me it was back in the player inventory when I lost after a fast travel.