Mail gone after clean install of El Capitan

Solution 1:

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:

1. Import every local mailbox from the backup
2. Clean up the mail boxes (Cryptic folders were generated inside every mailbox)
3. Add the POP accounts.
4. Write mails from there to get a dedicated "send" folder for each account.
5. Put the imported mails in the appropriate location (inbox, drafts, sent)
6. 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.