I have a lot that had a right of way from 40 years ago. It has never been used for anything. Can the city now come in and have rights, after 40 years?

The city always had "rights" since you did not go and ask for the right of way to be deeded to you. So yes, you may try and get a injunction to stop them and then go asking for ownership.

A right of way or easement is part of the recorded deed for a property. It is attached to the property in perpituity. However, if property owner made use of the right of way for their own purposes (i.e. fenced it off), they might be able to cancel the easement by right of adverse possession.