So I dropped my MacBook on a concrete floor and it was basically dead. Took it to an Apple store and they replaced the Logic Board and some other internal parts. (I have AppleCare. Whew!) They wiped my HD so I had to start new. I use IMAP email and when the MacBook went though it's set up routing I allowed it to "find" and set up the IMAP account. Now I have duplicates of every custom folder. I'm suspecting that the Mail app is confused because my IMAP syncs with my email provider service but is also syncing on iCloud. I notice that if I try to turn off Mail in iCloud and delete the mail Account to re-enter it, I receive a warning about Keychain and deleting the mail account on all devices. Not sure how to get delete the duplicate folders.