When using Zeus to edit a module's weather (Say, to make it super foggy/stormy), it will succeed on both the Game Master's Screen and all connected clients. If you then edit the weather to be clear and sunny, neither the weather or fog level will change for clients. The fog level appears to change for Zeus, but should Zeus leave and then reconnect, it will be back to the first edited value (in my example, the foggy/stormy weather).

The only way that you can edit the weather values again as Zeus seems to be to restart the server.

Additionally, editing weather as zeus overrides any mission-included dynamic weather permanently - it will not rotate out your settings ever.