I always refresh modifications after changes. see if the changes are taking place. If so then just add the mods back one at a time, refreshing each time, until then changes disappear then you will have found the mod that is overwriting the code(hopefully)
I think Opencart definitely needs to move to plugin architecture, event driven system, and a nicer MVC implementation which has now become the standard for web and it doesn't have to be from scratch it can just adopt a framework. And I'd love to be part of something like this.