I imagine that Woundwort's loss and almost complete destruction of his army would be a pretty traumatic experience for the remaining rabbits of Darkhaven. Think about it. They had been preparing for the return of Dark One, who would lead them to glory (and maybe to better living conditions) and he did. Then he took the whole army of Darkhaven to fight a war against Watership Down, which would surely end up in great victory and it nearly did.
However, after a few days Granite and Vervain return (maybe with a few other surviving warriors) and they tell a tale of defeat at the paws of Black Rabbit of Inle. Many rabbits would find that hard to believe at first. After all, who ever heard of Black Rabbit actively intervening in the matters of the living? He is supposed to only take dead or dying rabbits to afterlife, not fight in rabbits' wars. Some may disbelieve survivor's tale of defeat entirely, expecting Woundwort and the rest of warriors to return eventually. Some may question survivors' honor and call them cowards who run away from battle. Some may believe Woundwort lost, but think he was defeated by Watershippers, while the story about Black Rabbit coming down to destroy Darkhaven army is just a mad talk of battle-shocked survivors.
Most rabbits of Darkhaven would probably wait a few days, hoping that their warriors will return, or they would send a Wide Patrol to confirm or refute survivors' tale. Either way, it would eventually sink in them that Woundwort and warriors are truly gone. Now, Darkhaven might not be a place full of sunshine, rainbows and smiles, but surely those remaining had some friends (or maybe favorite Battle Pit rivals) and/or mates amongst those who stopped running. There would be a lot of mourning and despair in those days. Many would lose their faith in Darkhaven, because the prophecy that promised glory turned out to be a lie.
After that phase of grief, other feelings would come up to the surface, like fear and confusion. Darkhaveners would remember that rabbits from Watership Down are still out there and they would fear that Watershippers are going to attack Darkhaven in revenge. This would partly feed their confusion. They would be asking themselves whether they should stay in the warren or run away? Should their continue to wage war on WSD on their own or should they try to make peace with outsiders? Perhaps some rabbits would claim that Woundwort wasn't the one that prophecy spoke of and so they all should keep waiting and prepare for the return of "true" Dark One. If Darkhaven doesn't fell apart and if Watershippers don't invite the remaining rabbits to join their own warren, then somebody in Darkhaven will become a leader as long as they will be able to answer confidently one question: what do we do now?
That rabbit will have to give Darkhaven a new goal and inspire hope. Personally, I think that the Speaker of the Past or one of her students might be best suited for that task. They know Darkhaven's history, which can be used as source of inspiration for remaining rabbits. As storytellers they are likely to be a good speakers and one of them may have enough charisma to convince others to her vision and lead Darkhaven into a new future. Of course, one of the surviving warriors might become a new Chief Rabbit by winning fights in Battle Pit, but after spending most of their lives on waiting for arrival of Dark One, they might not be used to thinking/worrying about long-time future. What is more, they will be pretty demoralized after their defeat at Watership Down, so the new warrior Chief might end up doing nothing or he could run the warren the same way it was run before the return of Woundwort, even if that might not make as much sense anymore.
To sum it up: this is going to be a hard time for Darkhaven and there are many possible directions the warren can go from that point. They can scatter around; then can join Watership Down peacefully; they can live day to day, going through the motions and waiting for next Dark one who will make everything better; they can change some of their ways and try to build a new future for themselves; and so on... It all depends on what kind of rabbit becomes their new leader.
I could even imagine Spartina and Bigwig going to Darkhaven, becoming Chiefs and bringing remaining rabbits to some better place to found a new warren. Then again, Darkhaveners might not be very accepting of enemy Captain of Owsla and a traitor as their new leaders, so that scenario is pretty unlikely to happen.
