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Permissions inheritance block on Exchange Org object in ExPDA

Installing 2010 in co-existence with 2003.

I was provided with a ExPDA report before we ran the /PrepareLegacy /PrepareAD / PrepareDomain commands and this report only had the usual link state suppression messages.

I ran the ExPDA personally afterwards and there was an update so updated it and there is the permissons inheritance block alert:

Access control list (ACL) inheritance is blocked for the Exchange Organization object (CN=Email Environment,CN=Microsoft Exchange,CN=Services,CN=Configuration,DC=domain,DC=com).

I have seen this before running the schema updates in the past and just allow inheritance as per the MS articles and all is well, I have not, however, seen it AFTER running the Schema updates.  Questions:

  1. No Exchange 2010 servers have been deployed yet as it is a staged approach
  2. Why was this not on the ExPDA before?  Was it the update that brings this check in or has it occurred because of the schema update?  I normally see this error before updating the schema and just fix it before the schema update - would fixing it AFTER break anything?
  3. Is it a requirement to run the /PrepareLegacyExchangePermissions command again after fixing this, or can I just enable inheritance within Exchange 2003 before installing the first 2010 box and that is enough?  I need to apply the registry fix and reboot 2003 first so I cannot see the security tab at the moment.

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