It does happen. Hopefully you have a back up of the Information Store otherwise, you can try to repair the store using the exchange server tools. This process is not always successful and even if it is successful you can end up with errors and mailboxes that have corrupted indexes.

There are not any tools or commands available to re-index the mailbox. Here is a solution that I found that fixes the index of the mailbox.

1. First open the “Exchange Management Console”.
2. Expand “Server Configuration”.
3. Click on “Mailbox”.
4. On the right side of the screen click on “New Mailbox Database”.

This will open up the wizard to create a New Mailbox Database. Next, enter the new database name and the path to where you want to store the database. Click on “New” which will create and mount the new database.

Now, we need to expand the “Recipient Configuration” and click on “Mailbox”. Locate the user that you are having issues with and click on that user (Hold the “Ctrl” key to select multiple users). After selecting the users, click on “Move mailbox” on the right side. This will bring up the Move Mailbox Wizard. Click on the “Browse” button to select the database you created above and then click “OK”. Click “Next” on the next window. Select the “Global Catalog” and “Domain Controller” and then click “Next”. On the next screen, leave “Immediately” checked and click “Next”. This will move the mailbox.

After the move is complete, repeat this process to move the problematic mailbox(es) back to the Primary database. After this is completed the mailbox will be re-indexed.

I hope that is you ever come across this issue this helps you resolve it.