What I usually do for this is to set up Mail to pop itself and only delete mail from the POP server when it's moved out of the inbox for the account. Then when you delete your spam in Mail it gets deleted from the server. It's very nice because I have two machines POPing from the same server, and I usually get mail on my MacBook first, so I can delete spam there and not have to deal with it again when I get home and check mail on my MacPro.

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