The film describes time as something that is varying and non linear. The lives of the two characters, Joel and Clementine, much like any other person revolves around the memories they form alongside other things. However, when their memories are erased, they begin to form new ones. These memories are not dissimilar to the old ones they had formed however, the time they take to form these is what truly matters if they ever are placed in similar situations.
Time for them had taken a huge jump into the future once their memories were erased. When you jump, you move forward, but, the the process in the middle is what you miss and this is what leads to forming your memories.
Their mind functions the same way, however, it is as though a part of them has instantly disappeared. This keeps growing back with time, but, it should restrict the evolution of their relationship however, it does not since in this situation it is just what they need and it turns out in their favour.