What happened to the dragons?

That's exactly the problem – it affects ALL maps, absolutely.

Most likely, the author intended for players to only play this specific map, and the rest are just side effects. Delete the map, and everything will be fine, or start a new game. I didn't delete it, so I still have the issue where, in the last mission for the Academy in Erathia, birds fly instead of the intended creatures, due to one of my edits in the editor.