Dovecot does not clear the subscription file from non-existent folders. 

Hi!

Thank you for your bug report. Unfortunately this is not a BUG, but mandated behavior by RFC3501, see last two paragraphs in the excerpt.

Aki Tuomi

6.3.6.  SUBSCRIBE Command

   Arguments:  mailbox

   Responses:  no specific responses for this command

   Result:     OK - subscribe completed
               NO - subscribe failure: can't subscribe to that name
               BAD - command unknown or arguments invalid

      The SUBSCRIBE command adds the specified mailbox name to the
      server's set of "active" or "subscribed" mailboxes as returned by
      the LSUB command.  This command returns a tagged OK response only
      if the subscription is successful.

      A server MAY validate the mailbox argument to SUBSCRIBE to verify
      that it exists.  However, it MUST NOT unilaterally remove an
      existing mailbox name from the subscription list even if a mailbox
      by that name no longer exists.

           Note: This requirement is because a server site can
           choose to routinely remove a mailbox with a well-known
           name (e.g., "system-alerts") after its contents expire,
           with the intention of recreating it when new contents
           are appropriate.