This weekend I brought our domino server down to do maintenance.
I shut down the server and did an OS copy of all my mail databases.
Next I ran a NCOMPACT -B -D on all of the databases in the mail directory. Now I have 2 users who have folders missing, not all of them but only some. I have verified that the folders were there prior to the compact, the documents are still in the database in the all documents view but discover folders tells me they are not in any folders.
Did you also check if the folder has prevent refresh set? I am not sure whether this is relevant here.
And what about the ACL of these db’s? Are the server(group)s included?
And for your information: a folder can be seen as a list of references to a number of documents. It does not hold any document, as a view would. So that the documents are still in the db is not strange.