Archive folders detached and disappeared.
Re-imported them from ~/Library/Mail/V2/Mailboxes/…
and found a nice workaround for the missing “import” folder problem you hit if you try to import nested folder hierarchies in one go:
Try to import .mbox files first – if you click on through, the import will proceed, but you’ll never see any “import” folder created. However when you next open the import dialogue and choose “Mac Mail” instead of .mbox, you’ll be able to see the contents of the nested folders, and drill down to the individual mboxes themselves. Import them one at a time, then drag them into a coherent archive structure once you’re done.