If you use "Windows Mail" under Vista and your emails disappear, don't seem to be there when you open them or refuse to be moved or deleted, your message store is broken. Here is how to fix it.
1. Close Windows Mail.
2. Back up the email you wish to keep. While rebuilding the mailstore shouldn't result in any loss of email, it is always better to be safe. The easiest way to do this is to take a copy of C:\Users\your username/AppData/Local/Microsoft/WindowsMail.
3. Click the Start Button and select Computer.
4. Navigate to C:\Users\your username/AppData/Local/Microsoft/WindowsMail.
5. Delete WindowsMail.MSMessageStore.
6. Open the Backup directory.
7. Open the new directory.
8. Delete WindowsMail.MSMessageStore.
9. Open Windows Mail to rebuild the mailstore database. It may take a couple of hours if you have a lot of mail.
10. Mail may appear in "Recovered Messages". Just move them from there to where you really want them.
11. If it has all gone horribly wrong, close down Windows Mail, delete C:\Users\your username/AppData/Local/Microsoft/WindowsMail and replace it with your backup copy.
WMUTIL
For the lazy or technically-intimidated there is a great little tool which can compact the database, remove empty files and repair corruption. It is called WMUTIL and can be found here .
Manual Recovery
Sometimes, mail just gets lost or confused. The good news is that within the Windows Mail folder, your emails are all saved as inidividual files that can be copied out manually. If you don't have hundred of sub-folders or don't mind recreating them, one option is simply to run Windows Search on that folder an copy out any files ending in .eml to a different folder. Obviously closedown Windows Mail before you start.
Now rename the Windows Mail folder to something like "Windows Mail.poo". Run Windows Mail and it will create you a new folder.
Do not copy your .eml files back into the folder. Instead, with Windows Mail running, select the .eml files and drop them onto the Windows Mail application (eg. into Inbox) and the emails will be copied into the correct place in the Windows Mail file structure.
When you are happy all is well, delete your copy of the .eml files and the Windows Mail.poo folder.
RE-INSTALL
If your Windows Mail is still truly broken, there is a good walkthrough on how to rip-out your mail store and start again here .