There may be a better was I'm unaware of, but if you don't mind restarting Opus then one way to do it would be to exit Opus, replace the config file, then re-launch Opus.
(Some config files can be replaced while Opus is still running, but not the global hotkeys one, due to how the hotkeys have to be set up.)
The second post in How to Exit Directory Opus has some commands and scripts that can be used to automate exiting and restarting Opus, and those work when launched from Opus itself (as long as they are not launched synchronously, of course).