I saw a post at http://drupal.org/node/62394 which was similar, but a little different from my case so I'll try a new post.
I have several Drupal sites like this :
http://site1.com
http://site2.com
..
http://siteN.com
They all separate MySQL databases (no "prefixes"), but they all share a common Drupal code base.
I have a couple contrib modules (Gsite and AdSense), and Democratica themes.
I don't think I have "primary and secondary" sites which are referred to in http://drupal.org/node/62394. I'd say all my sites are equal peers.
All the sites have their own settings.php file like this :
drupal-4.6/sites/site1.com/settings.php
drupal-4.6/sites/site2.com/settings.php
..
drupal-4.6/sites/siteN.com/settings.php
Each settings.php looks like this :
$db_url = 'mysql://drupal_site1:PASSWORD@localhost/drupal_site1_databasename';
$db_prefix = '';
$base_url = 'http://site1.com';
I read the upgrade instructions and video, but I didn't see much on mutliple site upgrades. Like the users in http://drupal.org/node/62394 I saw a blank screen after upgrade in most cases. A couple upgrades were successful, however.
It seems like you need to run update.php while logged in as user #1. This seemed impossible for multiple sites since once
you switch the code base to Drupal 4.7 you won't be able to log into other sites.
I did try running update.php with "$access" set to FALSE (forget exact variable name). This at least let me upgrade a