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Corrupted nexus has to be a full 6 mods with only 1 portal to get the points. If you run it with more than 1 available portal you dont get the nexus.
I can't find this info anywhere, the only thing I found is on the wiki that says that to access a corrupted nexus you got to have a 4 mods waystone.
In the article about Crystalline Core of Knowledge (the "quest" reward to gain atlas points), it is only written that you need to clean a corrupted nexus with the needed Tier.
BUT I found something on the Atlas passive tree page that says the different needed tiers for such reward are waystone tier: 3-6-9-12-15
Therefore I think the problem is that the
text of the quest in-game is misleading and we don't clear the required tier corrupted nexuses
Edit: I play in french, maybe that issue is just with some translation
I figured it out on my own. I also experienced completing the map and getting no points, on the corrupted nexus without a boss it would not even let me open the map without a full mod waystone.
I realised this myself and I now just fully mod the exact tier needed and it works everytime.
The servers are in a bad state right no so I dont know if this is intended or a bug but full mod waystone have worked for me.
