Cardinal rules.
1) Make a backup of all board files especially config.php
2) make a full database backup with phpmyadmin and check you made a copy of config.php
3) Double check you have that copy of config.php
That done it does not really matter about any extra tables and fields lurking in the database.
Download the full package and unzip
Rename your phpBB2 folder on the server.
ftp the complete phpBB2 folder to the server.
ftp the config.php file to the server to overwrite the one that is blank.
If this new install is newer than the last the run the file install/update_to_latest.php with your browser.
Delete the install and contrib directories.
Upload any styles that you had added before or some users may get errors
If all is ok after proper testing you can remove the renamed directory.
Jim