>Would there be any concerns with being compatible with each other?
>Also, what about genetics being shared both ways in the future?
You have no control over that. Odds are they will somewhat eventually, but the queen tends to fly quite a ways and the drones tend not to, so there's a fair chance they will mate to other drones anyway. But there is also the chance they will mate with drones from your apiary.
> Would you try to keep the feral hive pure line?
The natural order of things is that bees have many mechanisms to insure that there is genetic diversity. I don't think I'd fight that.
> I know they are survivor bees by being on his property for 3+ years with no chemicals or intervention of any kind.
> I'm not even sure if there are frames in the box yet.
Which might explain how they survived. :)
> The box is collapsing and needs to be replaced no matter what. Any comments would be appreciated.
Sounds like you'll need to do a cutout.