Some of the config data is stored in memory as long as Opus is running, and only read at startup. Other config data is read from disk each time it is used. For the former cases, restarting Opus is required (but may also cause Opus to save the config data it had cached, so you want to replace any config files after exiting Opus).
Note that Opus continues running in the background by default. Fully exit Opus (via File / Exit Directory Opus) to stop it. There's also a Preferences option to make Opus automatically exit when the last window is closed, if you prefer it to work like that.
(Also note that dopusrt.exe is not relevant here. That just handles desktop double-click, if you see it in task manager.)
The USB version behaves the same as an HDD install in these respects.