I've made two more rooms, create a new challenge, new gear and items. Now I think that all the side-stuff you could do at this point is completed, and I'll be able to go back on the main point story path shortly. I've also spent some time looking at all rooms with InfoPacks in them and making sure that when you picked them up, it would properly despawn them the next time.
I fear that there is still some InfoPack leakage somewhere, maybe in a cutscene where you get one or something like that, I'll have to figure that out one way or another, either by replaying the whole game or finding something randomly.
Time spent on the project so far: 489 hours
Currently working on: Advancing the story