Lost some apps during the update process. Lost my computer's wireless connection at one point during the process and had to resume once I got a connection again. Maybe this had a factor in the following, I don't really know.
Application Center disappeared.
* VZ Navigator no longer to be found, I believe this was a pushed app available in application center when I got the phone in May 2009.
* VCast Song ID gone also. It was a pushed app which showed up some time shortly after I got the phone, so no idea how to retrieve this either.
* App World lost. Downloaded it again and works fine.
All other applications appear to have remained on the phone, but were archived and had to be restored.
Backup was performed prior to starting this whole process, but I had to manually perform the restore operation from the desktop manager to get back my contacts and other info from the backup file ".ipd". I don't know if the apps mentioned above should have been in the backup file, but they don't show up now, so I'm assuming they were lost in the storm.