ok so here is the method ive been using on a rented server(this method can be adapted to all types of dedicated server) if installing for the first time skip steps 1 and 3 remembering to stop your server

1:unsubscribe from the mod you want to update (making sure to navigate to \steamapps\workshop\content\346110 and also \shootergame\content\mods and delete the mod folder with the corresponding id and the .mod file from your personal files (this is important))

2:subscribe to the mod wait for it to download then load the game to main menu and wait for it to finish installing(can take a lil while so be patient) then exit the game

3:stop your server then navigate to \shootergame\content\mods and delete folder for the mod with the corresponding id and the .mod file(if you dont have the files skip this step but still stop your server)

4: Open your ftp client and log in to your server. Navigate to \shootergame\content\mods both locally and server side, if the Mods folder does not exist on the server then create it, next, upload the local .mod file and folder to your server.

5.to add the mod to your commandline im going to assume you already have the basics set up for your server just add the id like shown in the example. If you are adding multiple mods after the first id add , then the next id and so on there should be no spaces

some rented servers will have an option called 'commandline manager' click it add new then just simply add the id into the box for mods

"TheIsland?Port=----?QueryPort=-----?MaxPlayers=70?RCONEnabled=True?RCONPort=-----?GameModIds=539464369?listen"

this is the guide i used to make my commandline for those that dont have 1
http://www.arksurvivalevolvedforum.com/viewtopic.php?t=8

an easy way to get the id for any mod is open the page in a net browser for example google chrome and the id is in the address

6:start your server.

If you have problems after trying this please feel free to friend me on steam and il help you troubleshoot your issues