Question: Ben Affleck first met Uma Thurman at a party just before he was offered and accepted the three year job. Surely he would have recognized her after having his memory wiped even if he could not remember any of the time they spent together.
Nick N.
16th May 2004
Paycheck (2003)
Answer: Do you remember every person you've ever talked to at a party? Didn't think so. His memory isn't restored back to perfect condition - he's still had three years to forget about details at the party. He remembers things like the origins of the deal because it was important.
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).