Thanks to Heiko of WordPress Deutschland and Code Styling Project who brought up the problem on WordPress Deutschland:
Users reporting me, that they are missing files, after they automatically updated to WordPress version 2.8 and there were a problem while updating. I checked out the WordPress Trac and found a brand new record, which confirms this: Trac ticket # 10140
What happened and what are the conditions?
On one hand, the upgrade process has to be so far that the files were downloaded and unpacked. If anything goes wrong after these steps (wrong write permissions, etc.), the upgrade process makes a rollback and usually clears the downloaded files without any problems.
So much for theory. The practice shows, however, in exactly this case, because of a bug, previous existing installation files accidentally get deleted too, so the blog will no longer work!
What to do if already happened?
The best thing to do is to upload the old version completely via FTP. If the files are no longer available, you may download the old version from the archives of WordPress.org.
You should also verify if the wp-config.php needs to be adjusted, because this may also be deleted.
What lesson did we learn?
It’s not just a phrase, when we repeatedly emphasize, before you upgrade:
1. Create a current backup of the database
2. Create a current backup of all files on your web server.
As convenient as an automatic update can be, there is always a risk. If the web server is configured properly and is maintained well, there shouldn’t a problem arise. But the most users do not know or want to know if that’s the case. Therefore, the safest way is still to upload the new version via FTP.
Anyone who knows how everything has to be configured, I mean the pros among you, will surely continue to use the automatic upgrade.
This problem will be fixed, according to WordPress Trac entry, with version 2.8.1, and automatic upgrade will work again without any problems. But we think it is very important that the WordPress-Team let the users know about the problem and not just fix it in version 2.8.1 and be quiet about it. It will avoid a lot frustration!
But please don’t forget about your backup again, when you use 2.8.1 or future versions. It’s better “I have” than “if I would have”.
We still hope that you all continue to enjoy WordPress as we do, and we will continue to do our best to contribute you as quickly as possible with new information.