I am a Server owner/Admin of 13 servers on 3 different hosts, including a dedicated box at home. And have been doing so for Ark since Launch. Also, I work for modding team in Ark that is looking to create a TC. 

The issue here is not the devs, or the client. It is 100% a SteamCMD issue. Let me explain. DnL is a Total Conversion of Ark. It is a Mod per say. This is an important thing to know. Because it changed the way SteamCMD caches the game. 

In Ark SteamCMD keeps a cached copy of all mods installed on a server node. So if there are 50 servers on a node and over each has 5 unique mods, then there will be 250 cached mods on that server node. Now, each server when updating checks the mods it has installed against the mods in the cache. Then will copy over the files that are new or changed to the server. Before that, SteamCMD, once ordered to do so, will update all mods on the server node. And this is where the issue happens. 

SteamCMD, does not have a check system in place to see when items are deleted from a mod. Especially collision when separated by layers in ADK. We have had this happen numerous times with modded maps that either changed an area or deleted something off the map. The Landscape and all foliage will appear ingame, but the collision from the deleted items would remain. This would cause dinos to walk in the air, or entire blocks of an area have an invisible wall surrounding it, preventing players and npc's alike for entering it. 

The solution for Ark was to delete the cached copy of the mod, and the one on the server. Then manually copy over a fresh cached copy and server copy. (The Cached copy is compressed, and cannot be used on a server or vice versa). 

With DnL, This will be a little more complicated. The steps I have done to correct issues like this in DnL are as follows. 

• Copy the entire Saved folder and back it up somewhere.
  
  
• Wipe the entire server, including SteamCMD. 
  
  
• Install a fresh SteamCMD, and a new DNL Server
  
  
• Place the Backup you made earlier of the Saved file back where it should be. 

For now, I know of no other way this can be resolved. It is not a game developement issue. It has to do with the Steam API that handles file changes and deletions in updates. 

If you are using a host, you will have to have them do a complete wipe of the server after you have backed up all your saves via FTP.  DO NOT TRUST THEIR internal backups. 

Now, there is a small chance I could be wrong in this because DnL is a TC mod packaged as a full game. Some files are in the mod folder while the Map files are in the Content folder The chance is very small, but could happen. So I say this, try the above at your own risk. I cannot be held responsible for any or all issues that can occur.