If that is something you'd like to avoid, I'd recommend synchronizing them against different mailboxes that contain the contacts for the specific device. You can do this by creating two mailboxes and setting up the required MAPI profiles on the computer where the synchronization software is installed. You should then be able to select the "default" profile that each application -- and corresponding mobile device -- will use. You can also manage both mailboxes from a single profile in Microsoft Outlook, thus still making it easy to update contacts in the mailboxes.
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