If email is intermittently not appearing in the Inbox, then the problem is most likely occurring because of a corrupt view index. If this is the case, then running updall -r on the mail file will resolve the issue.
This problem has also been known to happen if more than one ($Inbox) exists in the mail file. One way this is known to occur is described in the following document: " Double Inbox is Created When the Design Task Runs on New Databases That Are Not Yet Initialized" (#1089921).
Additionally it may be possible that the different replicas were inheriting the design and one of the design templates was modified.
1. Go to Domino Designer and open the mail database.
2. Check if there is more than one $Inbox folder.
In-place with file size reduction -B Uses in-place compacting, recovers unused space and reduces file size,
unless there's a pending structural change in which case copy-style compacting occurs. If you use transaction logging, do full database backups after compacting completes.
In another case, this problem occurred in a mail file that had only one ($Inbox); however, the ($Inbox) view was corrupted. In that case, the issue was resolved by doing the following:
1. Created new folder called TEMPINBOX.
2. Selected all the current INBOX items and moved them to TEMPINBOX.
3. Using the Designer client, deleted the $INBOX design element.
4. Replaced the Design on the user mail file.
5. Sent new test message and mail now arrives in the new INBOX view.
6. Copied mail to new INBOX from TEMPINBOX folder
Caution: Beware that when the $Inbox folder is deleted (as is recommended in the next step), users will lose documents that are in the $Inbox. To avoid this, they should move the documents in the $Inbox folder to another folder (for example, Testfolder), and then delete the $Inbox, and replace design as specified to have only one $Inbox. Then, move the documents in Testfolder back to $Inbox.
3. If there are multiple $Inbox folders, delete them all.
4. Replace the design with the server template (by selecting File -> Database -> Replace Design, and specifying the template on the server).
In one case, a customer was able to resolve this issue by running compact -B on all affected mail files.
