That's an interesting query.. I guess I'd say a lot would depend upon how we define the word "population" as well as whether we are talking present realities in a given watershed in terms of sediment loading, temperature regimes, etc. as opposed to what these conditions were like in the days of people in three-cornered hats and powdered wigs.
So, I'll frame it this way. I'll define "population" as sufficient brook trout to be comparable with the wild brown trout pops currently in place in terms of biomass. Additionally, I'll go with the way things are today (or at least the last time I saw these places, since it's been a few years).
To that end, I have a hard time believing brook trout would meet this bar in the following limestone drainages (freestone portions excluded):
The Honey/Kish watershed. Spring Creek, including Logan Br. and Slab Cabin, etc. Clover , Piney and the Frankstown drainage. The (as noted) Penns watershed. Yellow Creek and tribs. Probably Spruce and the Little J.
I don't know enough about the Lehigh Valley streams to include any of them, but I have my doubts there as well. They are all pretty urbanized drainages with all that goes with that. I would say that in general the same would apply to the Cumberland Valley streams
My view would be that the mere presence of browns, even in a dominant role, is not in itself sufficient to preclude brook trout from at least being present in these streams, even if not in abundance. I'm not even sold on the notion that the presence of browns, even a strong brown trout pop., precludes the presence of a viable brook trout population. Here in the Midwest, there are quite a few streams with pretty potent brown trout pops. where healthy brook trout pops. co-exist in sympatry.
So, I tend to think that if conditions were ameanable to wild brookies in these waters, we'd see them, even if, as usual, they occupied the lesser niche.
I think you can go home again, if you really want to. But we shouldn't be surprised if it feels less like home than it once did and that somebody has moved all the furniture...