Make a copy of your phantombot.db locally (like on your own computer not the VPS). Terminate phantombot on the VPS, so it’s not running. Delete the phantombot.db from your VPS. Once you restart the bot, it should take you through the setup process.
If for some reason, it doesn’t take you through the process, you should just delete the installation from your VPS and start over.
As long as you have your phantombot.db file, all your data is saved.