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The military has the discretion to accept or decline a person based on a criminal history, even if that history has been dismissed or expunged. As you've found out an expungement does not totally erase a person's criminal record. It erases it to all persons and entities except for the federal government and its branches. Therefore, it will always be on his file in those circles.
He really cannot do anything about this, other than to enlist with a branch of the armed services that will accept him.