So the "/merged/" copy appears to be the one that I needed to modify. Not sure it was necessary, but I stopped and restarted the docker instance of dokuwiki.
Also, some code blocks did not show the change unless I edited and saved them again. That may be a caching thing that corrects itself over time.
Also note that ...geshi/sql.php will most likely need to be modified again if the plugin is ever updated.
Note: I found the file using $sudo find / | grep geshi/sql.php