> wonder if there has been a significant loss of institutional knowledge on how to make a lot of those old hand made animations
No need to wonder: there has been, and basically all Disney 2D animation, even what little they do for the cinema, is outsourced overseas.
On the one hand, yes, but also consider that game animation is fundamentally different from cinematic animation. It often has to be modular and loopable, but that also means that much of it can be treated like anime's "sakuga" stock footage (high quality, because it's going to be seen a lot). Cuphead was also something of a passion project, and the studio insisted on studying and replicating the older techniques to the best of their ability.
Basically, reverse engineering that process is probably a more expensive undertaking than most studios are willing to take. Look also at the Cuphead animated series, which was animated like a modern production (sadly).
Wasn't Cuphead done in the traditional hand-animated style, using many of the original techniques?