Nav Link Proxy SmartLinkReached event caught by wrong Nav Link

Hey,
I’ve stumbled on exactly this error in UnrealEngine 4.27.2 in my project.
I tried to override the RegisterCustomLink() in C++ creating a child class:
UMyNavigationSystemV1 : public UNavigationSystemV1

Not sure how to then tell the engine to use this new navigation system.
Changes in DefaultEngine.ini, like this:
[/Script/Engine.Engine]
NavigationSystemClassName=/Script/MyProject.MyNavigationSystemV1
have no effect.

Any ideas how to configure this?

Cheers,
Bartosz