If the soul has free will, then it cannot have a second-soul to dictate to it. What is the problem with the first-level soul that can freely choose, perhaps incorporating that metaphysical information into its decision?
The problems arise when you start to think what influences the soul's decisions. Does it make decisions solely based on its state? Then you have determinism. Not only state? Than what is this not-state that creates the free will? Adding some dice throwing into this mix does not sound like free will either.
That applies if you think of a soul as ‘just another mind’, but my understanding is that souls are usually seen as different. What I find problematic with them is that they can be defined to be whatever you need to get out of a logical fix eg “souls use state but are non-deterministic”.
Ultimately you’re asking what defines a soul, which is unknown as far as I can tell.
Ultimately I am asking what defines free will. The attempts at definitions that involve soul seem either circular ("soul is that part of human that has free will") or an unnecessary step, i.e. the considerations about soul might as well apply to original human, without the attempt to define a separate soul.