There is no easy way to import messages in the new 10.4 format (individual XML documents with the emlx extension) into Mail.app. It is not one of the options in Mail 2.0’s “Import” menu.

But you can put deleted messages back (if you have them in a backup) or add news ones and force Mail to reindex them. Here’s how:

1. Quit Mail.
2. Make a backup of your complete ~/Library/Mail folder just in case, by Option-Dragging it out of the Finder window onto the Desktop.
3. Create a new directory in your ~/Library/Mail/Mailboxes folder called – for example – “backup.mbox”.
4. Create a sub-folder in the new folder called “Messages”.
5. Copy all the messages (emlx files) that you want to restore from your backup into that sub-folder.
6. Launch Apple Mail. The mailbox you created will be in the list of mailboxes on the left. Highlight it (it will appear empty but isn’t really) and choose “Rebuild” from Mail’s Mailbox menu.
7. Mail.app will rebuild and re-index the messages.
8. When the process is complete you will see the messages you added in the new mailbox. You can then move them to wherever they really belong.

This has worked for me. And I double-checked it again this morning.