I came across the post as I'm in a similar situation. For me I fortunately had previous mysql dump unfortunately not too recent though. Currently I'm restoring back the Mysql dump and for the period of mails I don't have, which is like 2 week, I'm posting it back to the user from the store folder using the following command: zmmailbox -z -m email@example.com addMessage /Inbox /Restore. This seems to keep the date of the messages. What I was wondering though if there is a way one could have zimbra re-map the store folders that are not recorded in the MySql db. Say for instance you have /opt/zimbra/0/11/msg/0 1 2 3 4 recorded in the db but not the additional sub folders that was created after the mysql dump e.g. 5 6 7.