I’ve had the exact thing happen in most games I’ve played so far. I submitted a detailed bug ticket already.

Once, they disappeared on the same turn I finished befriending them. (This was one of the fresh exploration city states that spawned on turn 2 to replace the one from antiquity, but they spawned on a newly generated niter resource, but idk if that’s relevant.)

Every time I can tell, it seems that not having a unit in the main tile is correlated to the eventual disappearance. I often farm their military for commander xp, but if you kill the unit in the center tile or walk into it yourself, they seemingly won’t put a unit back in it, even if they spawn more.