Hopefully I can explain the issue a bit more clearly this time. Scenario - user has re-organised his shortcuts. Originally they were all dumped in one folder. I'll talk about a single mail, but there's about a thousand in this state that I know of.
Doing an advanced find in Outlook for the mail finds the shortcut in Folder A
Going to the folder in Outlook, finds the shortcut in Folder A
Doing an EV Seach of Vault finds the item in Folder B
Doing a seach in Archive Explorer, also finds the item in Folder B
Originally Folder B was not visible in Archive Explorer, even though a search tells you the folder exists, so you could not navigate to the folder that held all the mails.
The new folder structure the user created (Folder A) is visible in Archive Explorer, and shows the mails that have been archived from there since he did the re-org, and not the older stuff (as you would expect)
I tried recreating Folder B with the same original name and location in Outlook, and that is now visible in Archive Explorer, but has no mails under it.
So, the upshot is that EV knows that Folder B exists and has thousands of mails in it, but Archive Explorer does not show it.
Ideally, apart from fixing this, I'm looking for a tool to re-align Vault location with current shortcut location (I'm told that one does exist), as the next step is to get rid of old shortcuts. The only reason I found this issue was that I was showing a colleague what the plan was, and how Archive Explorer allows the users to navigate through a folder structure to find mails, only to discover the 'missing' folder. I have no idea how many other users are affected, as users currently use their bloated shortcuts....