Well, you can't readily, but it's easy enough to either use a separate configuration directory (Geany's -c switch) or write a short sed command to alter the configuration before starting.
These of course need Geany stop and restart, they can't be done while Geany is running.
…Or possibly write a small plugin that would change the color scheme depending on the time, or some other global setting.
And this needs coding, pull requests on the geany-plugins repository welcome :grin: