Additionally, the XDG folders ~/.cache/audacity, ~/.local/share/audacity and ~/.local/state/audacity are used on Linux.
Hint: These folders usually are hidden by default. You may need to show hidden files, or access their path directly, to access them.
You can delete all contents of the folder to get Audacity back to "factory settings". Alternatively, you can also only delete certain elements of it:
audacity.cfg is responsible for all preferences
pluginregistry.cfg contains a registry of all plugins and whether they can be used.
pluginsettings.cfg contains last used settings of effects as well as user presets.
Additionally, you may find some other files and folders there, eg. for macros, custom themes or plugins. These can also be deleted though, typically deleting the audacity.cfg and pluginregistry.cfg is enough in most troubleshooting scenarios.