I'm leaning towards the memories being there, but hidden in his own mind. The mind will go very far to protect the psyche (angel assistance or not), but with what he's been through, the memories are starting to form cracks and leak though.

I don't think even Dean knows if what he's getting glimpses of is real or not. Probably the more he thinks about it, the more it will come back to him, and he doesn't want it to be in his conscious mind.