SS doesn't require to be first in the load order.
However mods that add resources or dinos should be higher than SS in the order.

Structures disappearing is typically a failure of your server to properly load a mod before it loads the world. This isn't normally something the mod itself has any real control over.

It is normally associated with SP when they load into a world without allowing mods to be installed following a mod or game update...

For servers it can still occur but is much rarer.
Apart from making sure servers are safely shutdown and installing updates and mods carefully... There's not a lot you can do to prevent this.

The only real thing you can do is keep regular backups for when this happens that you can then revert to

Thanks for the information!