I've had a lot of fun playing with this planet, it's really well done. And I was looking forward to going back later on in the playthrough.

When I go to Nauvis from Lignumis, some chunks of the world will just stay black. The fog of war won't remove itself when I walk up to it.

I haven't seen this mentioned here, and I play with a lot of mods, so it's probably a specific combination of mods that makes it happen. But when I turn off Lignumis it fixes the problem.

I suspect it is a conflict with Resource Map Label Marker, since it seems to happen around patches of ore.
If anyone can tell me how to find out exactly what's causing it, I'll try to figure it out and update.

What the? Can you provide me a savegame (maybe on Discord if it makes it easier for you).

Sorry for the late reply. I deleted Lignumis mod first to start a new game, but then considered that I enjoy it too much and would rather play without the ore patch revealing mod. So I deleted that and tried again with Lignumis, and the problem was solved.

So, I guess the issue is with
https://mods.factorio.com/mod/resourceMarker

I noticed that, when landing on Nauvis, a few chunks get charted and revealed, since resource marker does the same, I bet the issue is with the double charting at the landing, both mods scanning the same chunks and then probably corrupting a few of them or something.
I had the option to reveal adjacent chunks next to ore patches on.
The problem is solved for me.

Thank you. I'll probably not investigate further into that topic.