The equations can be very cumbersome and there are many variables. Forget about the exact equations for a moment.
When you develop a new application you need to know the entire size of the project. This means you would want to include the number of function points of the application plus any other function points that need to be developed. For example, you may need to develop a mini (temporary) application to assist with conversion efforts. So in the end, you would have the number of function points for the application to be installed plus any other functions you needed to develop.
When you have an enhancement project and you are going to modify an existing production application, you are concerned about two things. The first thing is the size of the actual enhancement project. How many function points is this project? The size of this project includes any added functionality, any changed functionality, and any deleted functionality. Also in an enhancement project you may have other functionality needed that is not directly part of the enhancement project.
Normally an enhancement project is the size of any (added functionality plus any changed functionality) x the value adjustment factor. The value adjustment factor normally does not change; there is normally no conversion effort, so on and so forth.
The second concern is how did the enhancement project change the actual production application. Is the existing production application larger than before? And if it is larger by how much? This would be any added functionality. Also you would want to know of any functionality that exist before and is larger after the enhancement.
In practice the size of the existing production application will be impacted by added functionality more. Many organizations learn that existing application size does not change much, but they are changing existing functionality.