When calling Bukkit.unloadWorld with save = true, the implementation method in CraftServer calls NMS ServerLevel's save method, with savingDisabled = true, which skips the actual saving logic of ServerLevel, meaning the world isn't actually saved properly.

A patch has been PR'ed to Paper to fix this by changing savingDisabled to false, this patch has been tested and doesn't break anything else from what I can tell on initial testing, and has now been proven to fix a bug where worlds weren't saving properly when unloaded through the API this way.