[Tichy]

LA R'lyeh produces insanity in its dominion, which causes weird effects, like random commanders declaring themselves prophets. It may be that you were leaving them alone and not killing off their freespawn and they got an acre of prophets all at once, boosting their dominion off the scale.

R'lyeh also gets random events (I think) that spread its dominion to random provinces.

If both of those happened at once it might produce the effect you describe.

Check the stats graph, was there a quick spike in R'lyeh's dominion?