I've not done this on NW, but I can tell you my experiences on other carriers. Generally speaking, in a situation like this, the refundable ticket will have a manual entry on the face of it that says something like "500.00 NONREF FROM MCO." It may also make the ticket non-endorsable, although I suppose this varies by airline. Obviously, the refund department will see this and prohibit a full refund (you may get a cash or credit card refund for the refundable amount, and another MCO for the amount that came from an MCO).

This is the same thing that is done when having a non-refundable ticket applied (paying the change fee) as partial payment for a refundable ticket. Some airlines, such as AA, solve this problem simply by having a rule that you can't have non-refundable tickets reissued into refundable tickets - this gets around having to make sure the reissuing agent puts the restriction on the new ticket.

Of course, all of this relies on the agent that does the reissue to put the restriction on the new ticket. I would imagine that audit looks for these things, and when an MCO or old ticket is surrendered for a new ticket, they make sure that the auditor's copy of the new ticket shows the restriction, and "educates" an agent that forgets to do this.

All of the above refers to the procedure with paper tickets. With electronic tickets, either the ticketing system handles all of this automatically, or requires that the eticket be printed so that the reissue can be done manually.