Once again there's a missing function in the creation kit it seems. There's a GetLinkedReference but no SetLinkedReference. There's a GetParentRef but no SetParentRef.

What could I do then? I want to set a npc's parent/linked reference to a specified object and enable that same object when talking to the npc about one topic, and then disable the parent/linked reference again when talking about another topic. I can't figure out how to do this.

i think the point is about this:

the main purpose of a linked ref as opposed to a property is not needing a property. if you'd _set_ a linked ref though, you'd need that ref as a property to do this. once you have it as a property though, there's just no point in making it a linked ref, as you can do whatever it is to that property in the first place.

(which is also the answer to your actual question: make that object a property, in the info's begin fragment, enable it, in the end fragment, disable it (or whenever exactly this should happen)