I knew there must be a catch with the upgrade to WordPress 2.2. Whereas everything seemed to be all right short after the installation I recognized today that all the linked uploaded files could not be found any more.
The reason for this seemed obvious. Since I followed the upgrade instructions to delete/remove all the existing wp-files replacing them with the new versions in the way that I removed the whole wp-installation replacing it with the new code. Given that all uploaded files are being placed in the wp-content/upload folder they could impossibly re-appear after the upgrade.
Fortunately I did a full backup of all my files and folders (and not only the customized once) prior to the installation so I could restore them pretty immediately after I discovered the issue. The next time I am pretty much wiser and will remember that the wp-content folder does require some special care.