Shorty: C'mon, don't be mean to the one that does everything for you.
Michael Jennings: If you love me, if you care about me, go. Have a good life. Remember me.
Shorty: Say one word about this hat, and I'm outta here.
Michael Jennings: If you show someone their future, they have no future.
James Rethrick: Michael Jennings is not a super agent, he's an engineer. but somehow he managed to escape from a double-locked room. How? Was it fate? No. Fate was on our side. That means someone who knew, changed something.
Answer: He does recognize Rachel from the party as well as when he when he saw her at Allcom. The only things he doesn't remember are the last three years of his life since starting the project. So, while he does remember her, the three years they spent together while at Allcom are a total blank. This recognition is shown when he meets with Porter who helps him escape.
But later, when he is going through her stuff, he says he doesn't remember her. Also, if he did remember her, he would have known it wasn't her when the imposter was in the restaurant (also no need to have the imposter try to dress like her either).