Mac OS X 10.4, Mail: Messages seem to be missing, or "Message has not been downloaded" alert appears when opening

Resolution

Use these steps, one at a time, until the issue is resolved. Note: If you wish to back up your Mail messages before troubleshooting, make a copy of the Mail folder on a different disk (but leave the original Mail folder where it is). The Mail folder is in your Home folder's Library folder (~/Library/Mail).

1. Try rebuilding the Mail mailbox where messages are missing or can't be opened.
2. Reindex all messages:
   1. Quit Mail.
   2. In the Finder, choose Go To Folder from the Go menu, and go to ~/Library/Mail/ .
      Or, choose Home from the Go menu, then open the Library folder, then open the Mail folder.
   3. Move the Envelope Index file to a different location, such as your desktop.
   4. Move any folders in ~/Library/Mail/ that begin with "Mac-", "Exchange-", or "IMAP-" to a different location, such as your desktop.
   5. Open Mail. Mail will reindex all messages. This process may take several minutes depending on how many messages you have in your mailboxes.
3. If the account uses POP, try reimporting the problematic mailbox as a "Mail for Mac OS X" mailbox. You can import from your mailboxes in ~/Library/Mail/account name, where account name is the style and name of your account, "POP-Mac," for example.
   
   Tip: Remember to select the folder that contains your mailbox, not the mailbox itself. For example, you would select the ~/Library/Mail/POP-account name folder.
   
   If this doesn't help for a POP account, try importing as type "Other" instead of "Mail for Mac OS X". Select the mailbox itself (for example: ~/Library/Mail/POP-account name/Inbox.mbox).