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Thomas Blom wrote:

the Capi_killScript just deletes the C object - it doesn't
free the thread in any way (there is no way to free the
thread created with lua_newthread).

Threads are subject to garbage collection and do not need to
be manually freed.

But luaFn2 will never finish - is this OK?

Yes.  It's no problem if a coroutine is not dead (see
coroutine.status) when it is collected.