I’ve had this issue a number of times myself, and know some of my clanmates have also experienced it.
I have a base near Scuttler’s shortcut. I often go to New Asgarth or The Black Galleon to find named / high level artisans to capture as thralls. Sometimes, I forget to repair the binding first and it breaks en route back to my base. If I switch to a new binding and attempt to re-bind the (still unconscious) NPC they have a tendency of bugging out and disappearing through the floor. It doesn’t happen every time, but enough that I’ve lost several high-level NPCs this way which is very frustrating after going to all the trouble of finding one I want and getting it most of the way home!
Server is “Official server #1001 PvE” for PC.