Today morning, When one of our user opened Lotus Notes client, no email was showing in INBOX, but all appearing in ALL DOCUMENTS folder. To fix this I issued following command and problem went away and INBOX showed all emails.
load updall -r mail\usermailfile.nsf
This problem also occurs if you have corrupted INBXO view , dual of them. To check this you ahve to open user mail file in Domino Designer, and lookfor two inbox view. If there are two inbox view, first create a temporary folder, and move all the inbox mails to this temp folder, now create both inbxo folder, and replace design, this will create inbox view, now move all mails from temp folder to inbox , simple is that :p
Tip: If the problem remains still, then try to replace the FOLDER DESIGN.
Also read this thread, it really have some very good information to solve this problem.