So early game I was freaking out a little when my Hunter discovered a den and got killed. However, it seems to work really well to have two or even more hunting shacks nearby to kill the wolves and continually harvest their meat. Haven’t lost a Hunter yet to wolves using this method and it’s a constant supply of more meat just like deer.
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I realized this after I destroyed the den near my town since wolves are effectively a renewable source of tallow and pelts unlike deer and boars.
Maybe wolves should also attack local deer populations to incentivize you to get rid of the den? It would also serve as a way to figure out where deer are located - follow the wolves, locate the deer.
As it is I have to carefully manage my hunter cabins so that I don’t remove too many deer from the herds I am hunting and remove the herd from the map. I usually disable the huts around 2-3 deer left so they have time to recover, but I never worried about the wolf den since I knew they’d pop back eventually.
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If you put the hunting circle so that it doesn’t fully engulf where the deer roam, but instead just have the circle edge just outside where the deer icon is, it seems to work fine. They’ll hunt the ones that wander into the circle but not clear out everything.
Indeed ! 
I’m playing all my games on the hardest difficulty were deer does not spawn so abundantly and incoming roaming wolfs have proved an amazing source of renwable food.
One needs to step to the challenge tho ( 1 hunter, or 2 will do the job )
As to deer getting depleted they usually respwan the next spawning season.
Yea so far on the hardest difficulty 1 upgraded hunter hut cant fully deplete 1 deer spawn (only depleeted it once i think).