I have no idea what happened here, as I've upgraded my WP install numerous times, so I'll just list all the things I did and then pray someone knows what's going on.
I tried upgrading to WP 2.2.1, using the steps listed in the install guide. Upon trying to upgrade the database, I got this error message:
Cannot redeclare register_sidebar() ...
(and then some other stuff I neglected to copy).
A Google search told me my theme (K2) was conflicting with the new widgets feature, and I had to go back and uninstall the theme. So I deleted the new files I had uploaded and restored from a backup I made prior to attempting the upgrade. (I'd copied the entire wordpress folder from my site, which I just replaced, so it should have been the same as before.)
I then repeated the upgrade procedure and was able to update the database. I go to my site, and all my posts are gone. I still see the posts on the front page, but every single internal link on my site now gives a 404 message. (Not the custom WP 404 message, but the generic one you get at most other sites.)
You can see for yourself if you go to http://www.ryancoleart.com/wordpress and try to click on any of the permalinks.
So, I decided to revert back to WP 2.1.3. I deleted the new files again and restored from the same backup. I then restored my database following the instructions here.
No luck, the links are still dead. Does anyone have any idea how I can fix this? I can't think of what I might have done wrong, so I have no idea where to begin trying to figure it out.
edit: Never mind... it all appears to be working now. But I still can't get the 2.2.1 upgrade to work.