Yes, it's possible. The only time I've seen it happen personally is when someone deletes the last table occurrence for that table on the Relationships Graph. There may be other circumstances I'm not aware of.
I think your are right on. The table was not on the Relationship Graph, I added it, but needed to repair everything afterwards it. I thought it was missing in the backup I used to do the repair, but I was wrong: it was there, it's just I haven't use the button to show all of the TOC on the graph.
Removing a table from the Graph sure do a lot of damages .
"Removing a table from the Graph sure do a lot of damages ."
Yes, it does.