How can I recalculate a maildirsize usage value?

I have a few mailboxes that are using a different amount of space in qmail's eyes vs what the CP calculates with the "Calculate Box Size" features. For these mailboxes, the maildirsize shows a much higher usage number, certainly due to direct manipulation of the Maildir with rsync in the past.

I have tried many ways to recalculate that file, according to recommendations found elsewhere, but the file always comes back with the same values as if it is being duplicated from another source (perhaps the InterWorx SQL database). How can I accurately and permanently recalculate it?