Part of the process when migrating Cyrus IMAP accounts is running the reconstruct tool on the destination machine to add the mail to the database. Using the -r -f flags ensures, that the command will pick up any folders and subfolders.

Unless - as a client and I found out this morning - a folder contains no emails but just subfolders. In that case reconstruct ignores that folder (as well as its subfolders). To enforce its inclusion simply copy (any) cyrus.header file from another folder into it and re-run reconstruct (an empty file created with touch won’t work - it needs to be of this particular binary format that Cyrus expects).