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Vitali said:
The issue is that multiple-instance characters do need to be tagged in regards to their individual appearances--you would not have Marth_(Fire_Emblem_Awakening) and Marth_(Fire_Emblem_SD) as the same Marth--one is an illusionary clone in canon, the other is marked duplicate made using 'out of canon' logic in a different game. Marth is, however, his own tag as a unique and symbolic character, so one can easily forgo the two additional tags in this case.

Other cases, it would not be so simple--any character remade for Awakening, in my opinion, shouldn't be counted separate unless they are specifically edited to take on their own form, such as the Shadow Dragon (main antagonist of basically the entire series as I've seen). The Shadow Dragon goes by different names at times, and different incarnations and appearances--these should be marked as different tags. Sacred Stones, for what little I remember, had the Shadow Dragon differently from Awakening as an example.

It's entirely dependent on character-by-character stipulation from what I can tell.

So you're saying they're basically like LoZ characters?