The article [Q295965] states that when OE is started, some existing folders (Inbox, Sent, and so on) or personal subfolders may be missing and can be caused if the "Folders.dbx" file (the Indexer) is damaged or corrupted. To resolve this issue, simply delete this file for the impacted identity, and then start OE which rebuilds it. Additional reading concerning the "Folders.dbx" file, [Q233264].
CAVEAT: The Folders.dbx file also keeps track of Active News Group Subscriptions which are lost when this file is deleted -- you have to set things up again. This does not happen however when using the "Import" method.
Note: The Folders.dbx file categorizes and maintains the default mail Store display. When a .DBX file is copied over an existing file in the mail Store, in lieu of using the Import method, the Folders.dbx file would not of course have this newly copied file information in its index nor would the indexer be able to display the prior information since the indexer information and the file do not match, and you therefore get a blank box. To make sure things are in sync, if copying or moving files to the mail Store, is to simply delete the existing Folders.dbx file before starting OE. In fact, it's never a good idea to move or replace the Folders.dbx file since it's always regenerated by an OE start, which re-categorizes the existing Store folder mail.