So the conflict in Twilight's mind would be: I know this guy's counterpart from another world, but do I know the one of THIS world?

You know, if you think about it, the one that Twilight kept blushing over and stuff was Human Flash Sentry, that is totally unaware of Pony Flash Sentry. And as far as Pony Flash Sentry he interacted with Twilight exactly two times, and both were just bumping into each other. Pony Flash never danced with her, never proved her innocence to Vice Principal Luna, or anything else.