AVA
With everything that has taken place so far, I had made a conclusion. It would actually be better if Rafael does not regain his memories. That way, he can remain oblivious to the things that already happened and to the things that will continue to happen.
As he was yet to understand the things going on around him, I'm sure that he was confused and felt like he was in the dark. In my opinion, though it was a struggle, it was the better option for him.
Right now, Rafael was in a safer position compared to him knowing the things which I had already told him in the past. And even though he was under Marcus Zephanie's custody right now, it was better for him. That way, neither Marcus Zephanie nor X had a reason to cause any more harm towards him except for torturing me. But for that fact alone, I am rest assured that Marcus Zephanie would make sure that Rafael stays alive. He would keep him alive as long as he doesn't get what he had wanted from me.