AdminP creates does the Accelerated New Replica copies of the mail files, but they have not design elements. Unfortunately, if the Design task runs at 1:00. It can populate the design elements, while the replica is being populated at the same time. If you have say 500 mail files just created on a server, it is likely that between 5-10 will have two sets of Inbox, Drafts, etc.
Using the load convert task will clear the duplicate folders and seems to choose the correct (old) in-box folder to keep. You can also delete the one visible in the Notes Designer and the old one will then show up again. HOWEVER, if you accidentally delete the wrong one, you have to manually copy all mail from all docs back to the in-box, use the Folder(s) column in the view to figure out what goes back to the in-box.
load convert -r -u mail/filenm.nsf * mail85.ntf
The in-box folder gets corrupt mostly because the system time has been changed either on the server or on the Users workstation where a local replica copy exists and the user has replicated the mail file to the server.
One way to rectify the problem is to delete the in-box folder and then refresh the design of the database. You can also do a replace design over-top of the current one. In either case, the purpose is to replace the current $Inbox with a new one.
In-box corrupted by external force (backup hitting local mail file, when Notes client is running and mail file is in use.
The local client doesn't have a Fixup task you can run. However, you can typically also run compact which will notice and fix a corruption. If the mail file is on the server, run fixup first.
Optionally, you can blow away the current local replica with a new one from the server by overwriting it.