According to https://addon-docs.ankiweb.net/addon-config.html#config-json, plugins should store any data they want to keep around in a user_files folder in the root of the plugin's folder. Files stored there will be preserved when Anki updates the plugin version. Anki will delete any files stored elsewhere when the user updates the plugin to a new version.
We should, at some point, update the plugin to store its config.txt file in that user_files folder, otherwise users will have to rerun the "configure" step every time they update the plugin.