OK, I've been battling this for a while and haven't seen many posts on it, but here is what has happened and the best explanation seems to be a combination of iCloud sharing issues and this new "automatically maintain settings" in Apple Mail
- Mail interacts strangely with iCloud Keychain and Internet Accounts. Zombie accounts I've deleted keep coming back across all machines.
- Google additions don't seem to work if you have a previous imap setting so when you are say migrating to Google Apps, you get messages like can't find server when you are looking for the google server. You can use contacts, etc, but not notes and mail. Then if you wait a while it all works again. Strange!
- SMTP servers seem to lose their passwords and connection with accounts, it gets all scrambled. Again as if some sort of server master is overwriting local
- When you add a regular SMTP server, it forgets where the Trash is and you get messages like "Can't move message to (null)" there is a Mailbox command and you have to manually set "Use Mailbox For" to get this working.