Seems like a server management question, so I'd say the correct forum is
SRCDS servers.
sm plugins unload has to be run in the server console (likely over SSH and possibly in a screen / tmux session, since you're using a Linux VPS).
I'm not sure if there's a standard CS:GO multi-server setup so I can't give definite info there (personally I've segmented each of my game server installations), but
+exec your_config.cfg on server startup should work to load in a specific configuration.
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