Fine, I found the file just after I raised the question above. (It seem asking questions publicly stimulate me to search answers by myself much more diligently, since I don’t want my dear peers to view me as a lazy programmer.)
It is an XML file under /data/data/your.app.package.name/shared_prefs, and the file name is your.app.package.name_preferences.xml. It is really easy to modify the preferences when you figure out that the content is just a key-value map.