Mail gone after clean install of El Capitan
I decided to restore my mails by hand. That took me a few hours, but now I am back to normal.

Here is what I did:


Import every local mailbox from the backup
Clean up the mail boxes (Cryptic folders were generated inside every mailbox)
Add the POP accounts.
Write mails from there to get a dedicated "send" folder for each account.
Put the imported mails in the appropriate location (inbox, drafts, sent)
Add the IMAP accounts.


What I realized after going through all those steps, is that the accounts inside of ~/Library/Mail/V3 are not named by there account names anymore. Instead the consist of a cryptic combination of numbers and characters. Maybe that was the cause why Mail did not import anything.

My guess is, that accounts are now referenced by a number/character-code out of security reasons. However, that leaves me wondering how to do a proper backup of mail for a clean install.