Yes, they were included. All LL/Walthers engines were included except for the steam, which was "lost".
I imagine the old GP38-2, F-Something and 0-6-0T where permanently retired. I would guess we will never see the SD7/9 tooling wither since Atlas already has their version.
The F40PH is another hard call - the chassis was never updated and the roof details a bit crude. BUT... refinish the radiator fans, add flush fitting glass and a full pilot, the model would actually look pretty good. And a sound equipped F40PH might be a good addition to their commuter car line.
We will probably see the E series again at some point, but i was never a fan of the E7 or E8 nose. the geometry is all messed up and not easily corrected. The E6 appears better. I would also point out the E8 radiator area is not all that well molded. It was OK for the 90's, but wouldn't hold up well to BLI and Kato.
The GP38-2 can probably be folded into the current range pretty easily as it is a different phase. Wonder what they would do with the GP60? It's a good model, but not as good as FVM. Keep as is? Just add sound? Retool? Punt?
As I recall, Heljan tooled some of the early Walthers rolling stock. Specifically I believe the single sheathed box cars and the CO2 refrigerated cars. I hope these are with Atlas as well.