Well, if you know you're not going to use the old item for any sets, you can vendor it or put it in your bank. Then you can easily see which sets are missing items, and update them accordingly. If you have the new item equipped, then you can just equip the rest of the set and update it with quickly with one of the addons mentioned earlier in the thread, since the EM will just ignore the slot with the "missing" item.
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