Since upgrading to Mac OS X Leopard there are a number of blank emails within Mac Mail all dated 1 August 2008. I am unable to delete these emails no matter what I try. How can I get rid of these for good?

Other users who upgraded to Mac OS X Leopard found a similar problem upon launching Mac Mail, with several blank emails which could not be removed. It seems that the cause of this issue are phantom messages contained in the mailbox index file. Each mailbox in Mac Mail has an index file, which contains index information for that mailbox (such as a listing of messages contained in the mailbox). This allows email to be display more efficiently, as there is no need for Mac Mail to re-read every individual message when displaying a listing of mail in the mailbox, but rather it can read the index which provides reference to the relevant information and this can be displayed quickly for the user. Having phantom or corrupt entries in the mailbox index file could explain this behaviour, as Mac Mail thinks there is a message but there is actually no message, which is why selecting the blank message does not show anything. Additionally, you cannot delete the phantom message as it only exists within the index file and does not have a real associated message. The best way to fix this problem is to rebuild the mailbox index file. However, before completing the reindex we need to take some precautions. Some users have reported that a rebuild can actually cause more problems than it resolves, such as reports involving all messages in the Mac Mail Inbox disappearing. Accordingly, it would be a good idea to make a backup of the Mac Mail folder before completing the rebuild, just in case.

To perform a backup of the Mac Mail folder, first make sure that Mac Mail is closed. Then, open your computer’s hard drive and then the “Users” folder. Within the “Users” folder open the sub-folder that is named with your username. Next, open the “Library” folder. Within this folder you should see a sub-folder named “Mail”. This is the folder that contains all your mailboxes and mail stores. Copy this folder to a safe location, as you will need this should things go pear-shaped and we need to recover the data. As an aside, it is always useful to know the location of the mail store folder anyway, so that you can regularly backup this folder. Many people backup their documents and related data, but often forget to backup their email.

Once you have backed-up the Mail folder we can proceed with reindexing the email. Open Mac Mail and select the mailbox (e.g. Inbox, Sent Items) which contains the phantom email messages. Then, go to the “Mailbox” menu > “Rebuild”. This will proceed to rebuild the index file for the mailbox. Once this has finished, restart Mac Mail and hopefully the mysterious email messages should have disappeared.

In the event that the phantom messages are still present, it seems that the rebuild may not have fired correctly. In this case, we should try to manually force a rebuild of the index file for that mailbox. Close Mac Mail and return to the “Library” folder for your user account (as specified previously, when backing-up your mailbox). Open the “Mail” sub-folder. Within this folder you should see several files, with the name of the mailbox followed by the type of email account. For example, if you are using a MobileMe account then your Inbox for MobileMe might be named something like “INBOX.imapinbox”. Find the file for the mailbox which contains the phantom emails, then right-click on the file and select “Show Package Contents”. This should open that file so you can see the files which comprise that parent file. There are two files which are of interest to you: “mbox.SKIndex” and “mbox.SKIndex.isValid”. These are the two files which contain the index for that mailbox. Move these files to a different location (e.g. the desktop) so they are no longer present in that mail file. Once this has been done, start Mac Mail and the mailbox index should be rebuilt, hopefully properly resolving the issue. However, if you find that this causes more problems than it solves you should move the index files back into the mailbox file. This should put you back to square one.