Well, after the first one disappeared, two more spawned. I scooped them and dropped them back just to discover the species. They bred the trees really slowly, but no more butterflies showed up.
Nothing can be killing them, it's a closed space with no way out, except for a closed door, that I always close after leaving. The server just spent 14 hours running again and no new butterflies showed up. I've planted some flowers onto the ground (one from every type).
Also, I've never found a butterfly anywhere else in the server. No place else at all, and I've explored it A LOT.