This issue can occur if the Priv.edb and the Pub.edb databases have different DNs. This typically occurs if you install Exchange Server with an organization or site name that does not match the information stores that you are restoring, and you only restore either the Priv.edb or the Pub.edb database. When you try to start the restored Priv.edb or Pub.edb database, the restored database DN does not match the DN of the directory and the restored database logs the following event:
Event ID: 1088
Source: MSExchangeIS
Type: Error
Category: General
The information store could not be loaded because the distinguished name(DN)of message database
/O=org_name/OU=site_name/CN=RECIPIENTS/CN= does not match the DN of directory
/O=org_name/OU=site_name/CN=RECIPIENTS/CN=.
The database may have been restored to a computer that is in an organization or site different than the original database.
Note that only one of the .edb files is restored, and that the other .edb file has the correct DN associated to the current directory. This issue occurs because to troubleshoot this type of problem, you typically need to back up the Mdbdata directory, remove Exchange Server, and then reinstall Exchange Server with the organization and site name of the DN value that the event ID 1088 error message contains. When you install Exchange Server with a new organization and site name, the DN of the directory matches the .edb file that you originally restored, but the other .edb file DN is incorrect. When you attempt to start the information store, it logs an event ID 1088 error message in which the directory DN and the message database DN have switched from the previous event ID 1088 error message.