A word of warning...this question reveals plot points from season 3, episode 1.
In The Flash 3x01 "Flashpoint", the alternate timeline Barry’s in
starts to overwrite the reality Barry knows and he starts losing his memories of his life as The Flash
Transcription from a scene:
Thawne: And here, I was starting to think you'd forgotten all about me.
Barry: But I am forgetting. What's happening to me?
Thawne: I was wondering when you'd notice.
Barry: It's like I'll be thinking of a moment from my past and then it... It vanishes. I can't get it back. Why?
Thawne: Flashpoint. It's a side effect. See, I told you before. You don't know what you're doing. This new reality you've created is starting to overwrite the reality that you and I know. So your original life... Your friends, your family... Pretty soon, all of that will just fade away
Barry: Why isn't it happening to you?
Thawne: Not sure. Unless...
Barry: What? What? What the hell's so funny?
Thawne: Your speed! The more you use it, the faster you lose your memories.
Barry: No. No, you're lying. You just want me to let you out of here. That's never gonna happen.
Thawne: The you I know from the future, he's not this stupid. Pretty soon, you won't even remember that you're The Flash. And when that happens, this world will become permanent. Time will set like concrete, and nothing will be able to change it back to the way it was.
But at the end of the episode,
Barry decides to fix the timeline and then Eobard kills Barry's mom and the timeline is fixed; the events of season 1 and 2 still happened, although some are slightly different, for example Joe and Iris.
So: are all of his memories of
his old life — i.e. the events of season 1 and 2 — back in his head?