The point of the overrides system is NOT having to "hunt down" your changes. Your changes are in your override folders. You only have to compare the contents of the files in your override folders to the latest version of the same files and integrate the changes.

Mods/add ons may involve editing core files because an override isn't possible. For those, I create an override folder anyway and keep a copy of the changed file there. It won't be used by Zen Cart, but it helps me keep track of what I modified and what I need to look at when upgrading.