What happened to the buffalo during and after the war?

That's a very good question. Some people like the idea of Stalliongrad from Fo:E The Last Sentinel,

but that's just one small population of buffalo who were soon almost completely wiped out.
Why are there no buffalo Stables? It's almost like Stable-Tec didn't want the buffalo TO SURVIVE THE BOMBS

This is where my theory comes in:
We already know that Equestria offered bonds with griffons and buffalo to help out ponies in the war.
Griffons did whatever the hell they wanted,
and the Buffalo were said to have PLAYED NO MAJOR ROLE in the war!
Still, not letting an entire species survive the war you started just because they didn't help out much? Please.

What I think happened was the buffalo agreed with the contract with Equestria on their own terms. The ponies surpassed the limits they set in their own contract. The buffalo got pissed and revolted, ultimately losing. Then, for their acts of 'treachery', they had to sign away most of their land and were denied access to Stables

There you go.

Still, what do you guys think happened between the buffalo and ponies that would deny the buffalo access to the Stables?

I admit I never gave this any thought (seriously I thought about Changelings but not Buffalo).

There is, one slight flaw in your theory, Stable 3. Stable-tec built one for Zebras and another one for Griffons, I don't think they really would have cared about what the government said about the Buffalo and would've let them in a Stable. They where interested in the preservation of all life, not just the Ponies.

But I could be wrong.

5508818 Stable-tec happened. They aren't eactly the most loving ponies.

5508874
You're right, but how come buffalo are practically ignored in almost every Fo:E story?
There was no Stable build for the key purpose of saving buffalo.
Hell, what happened to the bull population when you think about it?
The bulls were mostly trouble makers, so why would Stable-Tec even bother to house them in Stables? They were a thorn in a rose that just needed to be removed.
That's believable, but then why did they do the same for buffalo?
They helped zebras who were the enemy!
They helped griffons who fought on both sides during the war.
Heck, I bet they even built a Stable or two for dragons!

So why were the local, and friendly buffalo tribes left to die in the mess that ponies started?

5509588 Maybe they're in an area not yet explored? I'm working on an idea for an area with more tribal lands than anything else, I could work them in along too.

5509784
Funny enough, I'm working with tribals too, their tribe is based in and off the cliff of the Forbidden Jungle. I thought that the idea could use some SDF certified Craziness, so I'm gonna have their tribe name be: The 'Iron Horses' and they worship trains located in the abandoned train yard somewhere in The Long Walk.
Since The Long Walk is also mainly plains, I plan on having feral ghoul buffalo herds running around the open field, and maybe some no ghouls, but that's all I can say spoiler wise.

5509821 Well there could be Buffalo survivors out there, so yeah. I'll probably work them into the Pinewood Valley Region somehow along with the Deer.

I think there was a deer settlement in the Everfree right?
I can see the Deer surviving the bombs (They used the tree magic!), and protecting the buffalo as well.