Ben Affleck plays Michael Jennings, a brilliant engineer. When he is hired to do a job for a man named Rethrick, he is told he will be paid nearly $90 million dollars. However, at the end of the job, he must have his memory erased of the job. Three years later, Jennings has his memory erased and goes to collect his $90 million dollars. However, instead of that, he finds an envelope with simple objects that seemingly don't connect together that he had sent to himself while he was working for Rethrick. The FBI come after him because of the job Rethrick had given him. Jennings has to find out what he was doing the past three years using the envelope and its contents.
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).