Yes, the scratches probably are from the fight. I’m sure she is a bit depressed about the whole situation. Making their set up so they can see and be near each other should help (which you have), but there will prob be an adjustment period. Is she eating and pooping OK? She might appreciate a “stuffy” to snuggle, just be sure she doesn’t eat it.
Spending time the same room as her but not directly interacting is a good first step. I like to play “hard to get” with shy bunnies. As prey animals, if you intensely focus on them before they trust you it can put them on edge. Hand feeding and spending time on the floor are also great ways to bond with a shy bunny.
Perhaps this will actually be a good thing, as you can take the time to bond with both bunnies individually, then when you re-bond them they will both be friendlier to you!
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.