So, I had noticed that some of the modules I had installed on this Drupal-based blog were out of date. Thinking it might be a problem with my Drupaldeb service, I started there. First, it appears that I might have a few bugs with ensuring that packages are actually properly put into the APT repository. There were two packages that were out of sync between the website and the repo. Need to fix that in the future.
But then I found the real problem. When you upgrade Ubuntu, it disables other APT sources. So when I last updated, it disabled the Drupaldeb APT repo, thus not allowing me updates. Simple task to re-enable that and voila. Modules updating.
After I had everything updated, I needed to update the database. That's when I made the fatal flaw of running
drush up instead of
drush updatedb. The former command happily overwrite my APT installed version of Drupal with 6.25 from the repository, which disabled a bunch of my modules. They even disappeared from my list of installed but disabled modules! Oh no, my website looks like crap!
After manually re-enabling the modules in the database (which didn't work), and downgrading Drupal again (which didn't work), I found the problem. When Drupal upgraded, it deleted everything from my /usr/share/drupal6 directory. Including my modules. So all I had to do was reinstall all my modules and themes and I was fine. This is something else I will have to test soon.