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Do you know where the other threads are blocked (more specifically the
thread that has its item collected)?
Yes. It is in C code after a return lua_yield().

Thread A
C -> lua_resume() -> lua_yield() -> C

Thread B
C -> lua_gc()

Thread A gets its stack trashed

 When you say "stack position 3",
are you counting from zero?
Sort of, I am referring to lua_gettop(L) type numbers,
in this case  lua_gettop(L)  is 4 and the 3rd item from the
top is et to nil.