Long story short, I am trying to edit the XML file "QuestDefinitions[MinorFaction]" in order to make a quest never finish within one of my current saves. It's the one where you scan a Ruins anomaly in order to assimilate a minor faction. I tried a few things, including commenting out the block of code that reads:

<Action_AssimilateMinorEmpire>

 <Input_Empire VarName="$CurrentEmpire"/>

 <Input_MinorEmpire VarName="$MinorEmpire"/>

</Action_AssimilateMinorEmpire>

But to no avail. Any advice on how I can make this specific quest just never resolve even if I do scan some Ruins?

In the part with all the prerequisites, add a path prerequisite that checks for "false" instead of an actual path.