> A. Attach/detach the thread around every set of JNI operations. This stops scaling really quick & gets super-complicated for writing error-free composable code (literally manifests as the problem you're concerned about with code flow changes resulting in silent bugs).

Sounds like a monad would be a perfect fit, assuming your native language is capable of that. That's how I work with e.g. JPA sessions, which are intended to be bound to single threads.

> At the end of the day you're actually also lying to yourself and trying to fit a square peg in a round hole. JNI is defined to use global state implicitly throughout its API - there's defined to be 1 global JavaVM single instance.

Of course if you're using an API that's defined in terms of globals/singletons then you'll be forced to make at least some use of globals/singletons, but I wouldn't say that's a case of singletons being "useful" as such. And if you're making extensive use of such a library, then I'd look to encapsulate it behind an interface that offers access to it in a more controlled way (using something along the lines of https://github.com/tpolecat/tiny-world).