A shame there are no replies to this yet. I'm having the same issue. Running Gentoo Linux on my server.
Prior to the game crashing with the error above I get a bunch of errors along the lines of.
14:01:55 [Server Error] Failed registering item game:helvehammerhead-iron: System.Exception: Attempted to register Item with code game:helvehammerhead-iron, but an item with such code already exists. Must use a unique code
at Vintagestory.Server.ServerMain.RegisterItem (Vintagestory.API.Common.Item item) [0x0005b] in <c29bb51c062d406599d97705b6ec16ba>:0
at Vintagestory.Server.ServerCoreAPI.RegisterItem (Vintagestory.API.Common.Item item) [0x00000] in <c29bb51c062d406599d97705b6ec16ba>:0
at Vintagestory.ServerMods.NoObf.ModRegistryObjectTypeLoader.LoadItems () [0x0006a] in <22e1ae0330ec45ec95af9c2d665e4262>:0
To make sure it wasn't an issue with old game data, I deleted my VintageStoryData folder and still get the same issue.