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I recently ran into this issue a couple days ago and didn't see a whole lot documented on it so I thought I would do a quick write up here. If you're trying to upgrade some of your site servers to SP2 and run into an issue, this should get you going again pretty easily.
Note: This article describes making changes to the primary site database. Before making changes in SQL Management Studio to the database, make sure to create a backup of your ConfigMgr 2007 Primary Site/Database. The process in this post has not been officially tested and is posted as is with no guarantee. This solution did work for me and it should also work for you, just make sure to back up your Primary site/database to be safe.
ConfigMgr2007 SP2 Setup on some Secondary sites failed due to insufficient disk space. Once we freed up enough disk space, we needed to get setup for SP2 restarted, preferably without having to copy the source files to the Secondary Site server and manually upgrading. Since the setup failed to even start due to disk space issues on the Secondary Site server, it got stuck in an Upgrade status and did not resume setup automatically even after freeing up the disk space on the server.
We found that manually copying the ConfigMgr SP2 source files to the server and running setup worked to get the Secondary Site upgraded, but if there are a lot of servers with the issue this can become quite time consuming. Since we did not want to have to perform this manual process on each server where disk space was already an issue, we devised the following solution:
Using SQL Management Studio at the ConfigMgr 2007 Primary Site database, we opened the dbo.Sites table and modified the Secondary Sites Status column from 5 to 1.
The Sites table in the Primary Site database will have entries for each site including the Secondary sites. In the database there is a Status column where the current status will be defined as 1, 2, 3, 4, or 5 :
Based on the above information, we changed the status back to 1 for the sites that failed , and then started another upgrade from the ConfigMgr 2007 Admin Console. This allowed us to re-trigger the SP2 upgrade without having to copy the files locally to each server and running setup manually.
Clifton Hughes | Senior System Center Support Engineer
I had a similar issue while deploying SCCM 2012 SP1 and used the above article as base for my Solution. My Secondary Site Upgrade failed due to a Pending restart. Post the Server restart the Status at the Primary Site was still Showing as Upgrading. I
modified the following fields in the dbo.sites Table
Status - 1
Version No - 5.00.7711.1000
All I needed to do was then re-initiate the Upgrade and Vola!!