Hi. I recently inherited a Drupal 6 site and used Drush to perform some pending updates, including core. It all fell to pieces, however, until I discovered that the site was built with Acquia Drupal and that the core update meant the removal of some Acquia provided modules in the root modules directory. I moved them out of there and into /sites/all/modules/ (after rolling back the previous updates) and ran the updates again. That seems to have solved the problem.
It should be noted that the site never used the Acquia Network Connector modules, so it did not rely upon Acquia for its updates that way, or for alerts about them. The previous administrator instead downloaded the upgrade packages from the Acquia website and manually applied them.
The updated dev site appears to be working fine, but before I deploy the changes to the prod site, I would like to know if there are there any flaws in my methodology or in my assumptions here. Any thoughts or suggetions would be most welcome. Thanks.