In this phase, you should make sure that you eliminate most of the useless stuff in order to make the upgrade process more efficient. There are many cases where customizations might not need to be carried forward into the upgraded destination system:
Older customization is no longer needed
The same feature is built into the standard NAV
The solution is already present in the market at an affordable price
New customization is preferred because of the poor quality of the older customized system
There can be other cases where you want to dump the idea of upgrading the custom code and/or object. The main idea is to filter those cases and only then move forward.