YouDied

It's probably something else. Please open up a support ticket or let me know your game server ID and I'll check.
 
    You've never had to do this actually. At server start/restart the server will automatically re-download and unpack every single mod. I know it sounds inefficient, but that's literally the only way to do it (Steam workshop is in it's infancy stage of being a reliable, automatable server-side product). So it's essentially mimicking directly the process of uploading an entire mod directory and .mod file to your server via FTP. To do a complete reinstall / wipe, you would simply just wipe all of the files/folders from /ShooterGame/Content/Mods/ without any need for uploading from FTP.   It appears that somehow the grabbing of files from Workshop -> downloading -> unpacking method is sometimes corrupted. This issue is prevalent with ARK client side as well, they even have a mention to that in their FAQ on their forums. Fun fact: we actually use the same C# code and built an executable off of code given to us from the server developer team at ARK to process our mod unpacking. So the logic/process is exactly the same as the client-side version.   I think when you are dealing with heavy disk i/o without proper verification (as it unpacks without verification) there is really no "check" to balance this out. If the disk i/o freezes up on the server and the unpacker executable crashes out (likewise with the client game itself) the mod unpack could be corrupted and lead to bad mod files causing wonky issues like this. Just one of possibly many imperfections with this process.   Sorry to get technical, but as you can see it's quite a difficult process to debug and following the aforementioned steps seems the best way to force it to work apart from any client-side issues that may be unrelated to the server mod files.

This is going to be toggled from the server control panel side. Working on it now.
 
EDIT: It's been added.