I think I know how I'll deal with it - in my main fandom where this is a concern, I have two distinct characters in two timelines that count as the "main character" of the game, and most of the time their relationships don't really overlap, with maybe one exception? And I probably wouldn't write a fic for each of them with that one character, by the guidelines, but I feel like I could do multiple pairings with each one because they're technically in the same role, in terms of the story. If that makes sense.
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I think I know how I'll deal with it - in my main fandom where this is a concern, I have two distinct characters in two timelines that count as the "main character" of the game, and most of the time their relationships don't really overlap, with maybe one exception? And I probably wouldn't write a fic for each of them with that one character, by the guidelines, but I feel like I could do multiple pairings with each one because they're technically in the same role, in terms of the story. If that makes sense.