Will my shop still work after upgrading from Open Source to Enterprise (Commerce)?

Our agencie asks for 150.000 € to upgrade our shop from open source to commerce. They claim that they have to recode the header, mega menu etc.

 

But I upgraded a test instance (clone) of our shop and It still works fine.

I have analyzed the vendor code before and after the upgrade and noticed that the core was not changed, there are just a few more modules and some “advanced” modules e.g. “module-advanced-catalog” which are extending core modules.

But will these extends break anything?