If the user is part of any AdminSDHolder group they will lose the send as permission.
Here is the complete list of AdminSDHolder Groups:
• Enterprise Admins
• Schema Admins
• Domain Admins
• Administrators
• Domain Controllers
• Cert Publishers
• Backup Operators
• Replicator Server Operators
• Account Operators
• Print Operators
If he is part of any of the ones above the best way to fix it is to a) remove the user from the group or b) run the dsacls script from
The "Send As" right is removed from a user object after you configure the "Send As" right in the Active Directory Users and Computers snap-in in Exchange Server