Yea, they arrive at the start of 2848. I believe the one beacon did not get discovered by them at all.
Would more save files or screenshots help?

I would like to add to this.
In 1.2.8.8 I had a pirate sell me the location of one the beacons and I set up a outpost on it.
20250215005239_1.jpg
After establishing outpost I did not get any message about capturing a beacon or was able to research it.
After the war started a defeated zenox empire ...

I captured a colony with a beacon before the portals even show up.
https://mega.nz/file/bK4BSRBS#xTUMjo0yCR4MIERcfLPVQSuTVotWL1rE5SOvy7Xt4JY This is a save as the planet is taken.

20250125081048_1.jpg

I was able to research the study/destroy beacon techs but the beacon was still there later into ...

I do have random research on and got no issues with missing out on entire tech lines but missing out on victory technology or planet destroyers can be upsetting.

I not sure if this a bug, but I don't think the zenox should miss out on a racial tech or objective.

Crew systems maintenance reduction overrides the star marine barracks.

I dont have any mods installed.
I should of worded my post better, I was talking about the weapon granted from the artifact.

The teekan experimental ion bomb overlaps the super ion bomb on the research screen and cannot be researched normally