[I collected all the previous posts on Malabou here in order to avoid constant linking the new post to the old ones, since these are simply reading notes, use them as you see fit, but preferred uses are: to impress someone with knowledge of Malabou without actually opening the book, to cite in defense of claim “I was into Malabou before it was cool” and the like pretentious yet awesome ways…]
What is this “cerebral unconscious” then? One must be careful, argues Malabou, not to fall into the trap of identifying that which is not conscious with that which is unconscious. “Cerebral unconscious” is all that information that brain provides for itself about the internal state of the organism, that it informs itself of, that it auto-represents, i.e. “cerebral unconscious” refers to the whole ensemble of processes of brain’s autoaffection.  If we go back to the introduction of this discussion of the relationship between sexuality and cerebrality, we will see that Malabou already emphasized the fact that “neuronal architecture is composed of different systems in constant interaction.”  This point should remind the reader, I think, that the discussion of “cerebral auto-affection” or “cerebral unconscious” is not directed as some sort of system-building that would reconcile the struggle between sexuality and cerebrality via some sort of larger synthesis of both into a final system.
What is the “auto” of this “auto-affection”? It certainly cannot be the self as the subject, since the distinction between the subject and the objects, is not yet established – not temporally, but formally, Malabou seems to suggest. It is a sort of a “cerebral identity” that allows one to speak of brain “seeing itself live” (le cerveau (se) voit vivre). This cerebral identity underlies (conditions) any subjective identity one might have: “If the subject is able to ‘touch itself’ it is only by the grace of the brain.”  But the brain itself never appears as a part of my internal awareness of myself:
When I write these lines, I see myself writing them, but such vision is nothing but the derived and elaborated form of primary autoaffection, to be precise, of cerebral autoaffection, constant yet invisible, that remains inaccessible to me, inaccessible in all its richness despite the fact that it is what precisely allows me to write. [paraphrase, 85]
This is what Malabou says others have called “proto-self” in its relation to the “self” which is nothing but a perceptive surface. Jaak Panksepp calls it “simple ego-like life form” – Malabou also refers to Freud’s discussion of self in The Ego and the Id. But what is the final point of all these details? Why is this notion of “cerebral aufaffection” so important at this point? Malabou wants to present this notion in order to, not unlike Derrida, one could say, problematize the “common sensical” idea of representation as having already established conscious core that does the representing: “The cerebral self represents itself without representing itself.” 
So chapter 1 (L’autoaffection cérébrale) ends with a short section on “temporal brain and destructible unconscious” that is aimed at establishing some sort of connection between the cerebral unconscious and the psychic unconscious we all love and cherish so much… This section is rather short and since the next chapter deals with the primary theme of the book – wounds, damage and so on – the transition seems a bit rough because the final sentence of the chapter addresses the issue of both temporality/destructibility of cerebral autoaffection (cerebral identity) and the subsequent suffering that is associated with this vulnerability:
The sole subjective experience that it is possible to have of cerebral autoaffection is that of suffering that comes with its damage and its interruption. 
Before I go on with the reading about cerebro-damages (les cérébro-lésés), I think it would be beneficial to go back to the introduction to the Part One of the book. The intro – The “new maps” of causality – attempts to situation the discussion (of the work in general, it seems) in the conflict between neuroscientific and psychoanalytic explanations of the various types of trauma: “the common point between psychoanalysis and neurology is in the task of thinking together the auto-regulation of the system and the disturbing intrusion…” So is the interruption of the cerebral auto-affection that makes it visible a kind of privileged entry point similar to Freud’s interpretation of the dreams? Malabou’s set up here is to look at cerebral trauma not only with a therapeutic agenda in mind, but primarily, it seems, in order to reevaluate the accepted philosophical, psychoanalytic and neurological concepts of self, life, suffering, and so on.