Me too, a lot more people had problems recently with the game and it is disconnecting for me each 2 to 3 minutes due to connection, but its just fine, it is the game probably, hopefully will be fixed really soon.

Yea, basically any DLC Animal you had in your franchise zoo when it disconnected would disappear, it happened to me and I stopped playing because of it. I lost 200 animals from one franchise zoo. I am not gonna open it until it's fixed, because that really bummed me out.

https://steamhost.cn/steamcommunity_com/app/703080/discussions/0/4031348734036134177/

I haven't lost animals, except yesterday. I would buy, but then either it'd disappear from storage or never appear.

In your case, if you ESC out of that popup you're playing without a connection that's likely why you lost animals. Your animals are on their server, not in your save. I never ESC out, I just leave it there until "resume" un-grays.

I have a new franchise, and my African Warthog couple simply disappeared, the habitat was empty and they are nowhere to be found in the zoo.

Apparently this doesn't affect sandbox cause you don't have to connect.