All my Mailboxes were orphaned when I upgraded to 10.11.1. Why this happened, only Apple knows. I imported the boxes back in. A typical mailbox now has mail buried in subfolder inside subfolder... sometimes to 5 levels of folders i.e. Mailbox/AE1B7E93-4902-4950-970A-C40F60BF2353/Data /6/4/1/Messages. Why, in the name of the Universe did Apple adopt this scheme? It has been this way for several iterations of Mac OS X. They have done this with iPhoto, as well. What ever happened to the idea of KISS? I saw no need or advantage for this kind of organization and I now spend a lot of time undoing this. Why has Apple taken this route?