Depends on how you installed the bot.
- If via apt-get, just perform apt-get update && apt-get upgrade
- If via manual deb install, re-install
- If via PyPI you may loose the rules.conf and settings.conf
- If manual via unzip/tar you would overwrite the rules.conf and settings.conf
So you may need to copy the content of /conf/ folder to different folder, replace all files and copy back the conf folder.
The database will never get overwriten !