On Friday March 21st my customized Outlook 2003 Navigation Pane Shortcuts were fine. On Monday March 24th I they'd vanished.
This has happened before. It's bad, because I really depend on these things.
I don't know why they vanished, though I suspect an update of some sort triggered an old bug. These things are known to be fragile in Outlook 2003. I resolved to come up with a way to restore and back these up, and with a bit of Usenet help I did manage that.
Here's what worked for me.
- Find out where Outlook stores this data: Microsoft kb: Outlook file locations  mostly answered that question. It says these customization are stored in: "drive:\Documents and Settings\<user>\Application Data\Microsoft\Outlook\Outlook.xml". There's an error in the kb though, the file is not named "outlook.xml". When Exchange Server is in the picture the file is named by the Exchange/Outlook profile. In my case that's "Default Outlook Profile.xml".
- I used our corporate backup software to find the most recent backup prior to when the truncation occurred.
- I saved the last 19KB file to a local folder and used a text editor to extract the portion with the tags: <userdefined> from the backup. Then I exited Outlook and copied it into the current version of this file.
- I then launched Outlook and added ONE new Shortcut to a store in my PST File. If you don't do this you get a "messaging error" when you try to use the old Shortcuts that point into local PST files. My guess is adding a new one forces Outlook to update some binary cache file it won't otherwise update.
I still don't know why my Navigation Pane Shortcuts vanished. They may have been a casualty of something that damaged another part of the "Default Outlook Profile.xml" file. I'll see if it happens again, but from now on I have a backup and an easy way to restore them when they get wiped out.
-- footnotes --
 It's astounding how long and complex this list is. Outlook is a very old and rickety piece of software. Slipstick also has a good reference list.