This has happened twice in the last 10 minutes. I'm working on parts of a large build composed of five pieces. Each time, it's happened like this: Edit linked part, move the part around, and then click on another part, and the whole object unlinks. Twice this has happened! Of course, the object won't go back together, either. Everything will link except the former, centrally-located-for-plotting-convenience root prim. Great.
I'm getting to where I'm going to start tweaking the main part. Is the 200-prim object going to unlink for no apparent reason and then refuse to go back together? Answer: Probably! Yay!
Update: The third tower unlinked. I'm just going to leave the fourth tower and superstructure alone. It's just not worth it.