A number of potential issues could be causing this folder disappearing act between Exchange Server 2013 and the Outlook Web App.
When troubleshooting a problem with Microsoft Exchange, start with the potential causes that you can eliminate. Since the connection in this scenario with an Outlook folder missing is to the Outlook Web App (OWA) virtual directory and not an Outlook connection, you can eliminate any potential Outlook client profile issues. While it's unlikely causing this problem, Microsoft eliminated Outbox as a folder in OWA in Exchange Server 2010 and higher. Exchange administrators ask about this on a regular basis. If Outbox is the missing Outlook folder, this is not a problem, it's by design.
If the folders that went missing were created by the mailbox user, the following steps might detect and repair the issue.
If corruption has occurred and this troubleshooting path leads to resolution, don't stop before you get to the root of the corruption. Investigate your storage setup to confirm there are no underlying issues.
Verify the user is on a compatible Web browser. Compatibility with OWA in Exchange Server 2013 is a combination of OS and Web browser. Windows 7 and higher combined with Internet Explorer 10 and higher will provide the best experience with excellent compatibility. However, Firefox, Safari and Chrome are also compatible with OWA. Even with a compatible browser, security settings and Web caching settings can mess with the user's ability to successfully view content in OWA. Clear the cache on the browser, and verify that the URLs to the OWA virtual directory are not being blocked.
In any troubleshooting process, you must identify the scope of the issue. It sounds like the issue is limited to just one mailbox, but it's a good idea to see if other users on the same mailbox database, Exchange server or network segment also have an Outlook folder missing, or similar issue. If you have a high availability architecture that incorporates multiple Mailbox and or Client Access servers and load balancing, try to narrow down which servers this user's mailbox communicates with. If it is not localized to the user's local computer then it is more likely others would be affected.
If the issue was related to a problem with the OWA virtual directory, the scope of affected users would be significant. If the issue was related to the Mailbox database, it is possible the scope could be as small as a single mailbox. If other users with mailboxes on the same database are not experiencing any issues, try the following commands to troubleshoot the folder issue.
Based on the results received when you detected corruption, run the cmdlet again without the –DetectOnly parameter, which will help narrow down the repair to the type of corruption that was detected. In this scenario, based on the missing folder problem description, it is possible the FolderView is the corruption type that is occurring in Outlook.
If corruption has occurred and this troubleshooting path leads to resolution, don't stop before you get to the root of the corruption. Investigate your storage setup to confirm there are no underlying issues. Use the –Database parameter with the New-MailboxRepairRequest cmdlet to see if other mailboxes in the same database have any corruption that users did not report. If you do identify more widespread corruption, try to fix the underlying root cause rather than depending on this cmdlet as an ongoing fix.
Next Steps
Alert Outlook users to completed mailbox moves
Causes of slow Exchange 2013 mailbox migrations
How to remove corrupt virtual databases
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