The names.nsf file on a user’s machine and the names.nsf on the server are not replicas. They will never replicate. Each database has a replica ID, which can be seen by users in the Database Properties on the second tab. If you review these on the two databases, you will see that they are different.
It is not a problem that they are not replicas, so you have no problem to overcome.
What is your role in this question? Are you on support staff at a company? If so, you should ask for training so you can understand the Notes environment, as this is basic to understanding how it functions.