I got a notice to upgrade to the most recent patch version - 1.2.26 (from 1.2.23). I forgot that you're supposed to uninstall the patches first!

So I installed the new JMS package through the Joomla installer and now my slave sites are controlling my main site (the global configuration is wrong and pointing to the wrong DB). How do I fix this? Right now there is no way to edit the subsites b/c any edits that are made take place on the main site, not the slave site.

I tried to just go to Manage Site > Site Name > and resave it but it gave me this error:

Error writing configuration file [/home/centra/public_html/services/baseline/configuration.php]

I am using suPHP so there should be no permissions issue.

Please help!

Okay, I think I have fixed the problem. I had to rewrite the configuration.php file for each slave site. But the question is, how did all the configuration files get rewritten with the main sites information???? This is concerning for future updates. Once we go live, we cannot afford to have issues like this so I need to know how to avoid them for future upgrades.

The only reason that I see is that you have enabled the FTP layer.
When the FTP layer is used, this is the FTP Root path that can be used to compute the path where the configuration file must be update.
In this case, this is the FTP that perhaps report that you don't have the access to the file.

No sir - the FTP layer is disabled on all my sites b/c we have installed suPHP on our server and no longer need to use FTP.