This is how the Exchange 5.5 gets email to the Exchange 2003 system. Email sent to Exchange 5.5 from Exchange 2003 is done via an SMTP redirect to the Exchange 5.5 Internet Mail Connector (IMC). We decided not to use an Active Directory domain controller to replicate the Global Address List (GAL) to the Exchange 2003 system.
Is there a way to export the entire Exchange 5.5 GAL and then import it into the Exchange 2003/Active Directory system -- which will also remove Exchange 5.5 addresses when they have been removed from the Exchange 5.5 GAL?
It depends on the frequency that you want to update the information in the target directory. You could use the export feature in Exchange 5.5 to get a .CSV export of your existing Exchange 5.5 environment. Once you have this, you can update the information via an import into Active Directory (AD), making contacts to mail flow.
If these updates occur fairly frequently, you should investigate the Microsoft Active Directory Connector (ADC), which can help with this type of synchronization work.
Can you provide more detail or links (maybe some step-by-step instructions) on how to export the .CSV and then import into AD?
Microsoft's FAQ on bulk importing and exporting mailbox data explains the process for extracting data from Exchange 5.5. You simply open the Exchange 5.5 Administrator program and click on Tools -> Directory Export. The article gives a lot more information about the options available when performing mass data management in Exchange 5.5.
To create objects in Active Directory (AD) -- with the exported information from Exchange 5.5 -- I would look at Microsoft's article, "How to use CSVDE to import contacts and user objects into Active Directory."
To modify existing objects in AD, you should read Microsoft's "Using LDIFDE to import and export directory objects to Active Directory."
—Peter terSteeg, Exchange Deployment and Migration expert
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