1) Unsub from mod (on the client)
2) Delete mod from both the steamapps/workshop/content/346110 folder and the steamapps/common/ARK/ShooterGame/Content/Mods folder. In the mods folder be sure to delete both the folder and the .mod file. (on the client)
If on server stop the server and delete the mod from the mods folder.
3) Resubscribe. (on the client)
4) Wait for it to download (on the client)
5) Start ARK and let the mod install (on the client)
6 - server only) Copy refreshed mod from windoze client to the server. steamapps/common/ARK/ShooterGame/Mods both the .mod file and the folder associated with the mod and then start the server back up.

IF using the automodupdater
(If using windows replace linux with win64)
1) Stop the server and wait ~3mins
2) Delete the entire workshop folder located at
Engine/Binaries/ThirdParty/SteamCMD/Linux/steamapps/Workshop
3) Also Delete the everything in the Mods folder except 111111111 and TheCenter folders and file.
4) There is a file called appworkshop_346110.acf just inside the workshop folder. Delete that as well.
5) Start the server back up. It will redownload all of the mod content fresh.
This should be done regularly anyway.