Yes, sadly, although you can still use the BCR allegiance and abilities, you would have to use the updated Warscrolls, and wouldn't have the Mawtribe allegiance abilities. This means no Trampling Charge, Might Makes Right, Ravenous Brutes, etc. with generally nerfed Warscrolls. Stonehorns can't run and charge, cause no impact hits and only count as one model for objectives, for example.
With the exception of maybe an entire force of Hunters and cats in a Skal, I can't see the old allegiance being effective anymore.