The nightly cleanup should only remove unreferenced data, unless you have no unreferenced data and are way over your memory limit.
You can also manually remove unreferenced data from your bot's Admin Console, Konwledge, Reports & Tasks page. Select "Delete Unreferenced Objects" and "Delete Unreferenced Data Objects".
To fully clean your bot, you can also create a new bot, and only import the scripts and responses you want to keep from your old bot.
