Glad I asked MichaelH, the upgrade instructions in 2.1.3 says the below which sounds like like you delete the config and everything. (except maybe custom themes)Perhaps it could be re-worded? LOL!
Thanks! I got it.
“Upgrading
Before you upgrade anything, make sure you have backup copies of any files you may have modified such as index.php.
Upgrading from any previous WordPress to 2.1:
1. Delete your old WP files, saving ones you’ve modified.
2. Upload the new files.
3. Point your browser to /wp-admin/upgrade.php.
4. You wanted more, perhaps? That’s it!”