I tried to look into what may be causing this and I am actually not sure.
Fortunately it seems that you already killed the first two bosses, so technically it won’t break the game that it disappeared, but very sad that it did.
Had you just reloaded the game? or did anything around it? did it somehow take damage? had you just upgraded it?
In this save file, I have only killed the Watcher. Reloading it doesn’t seem to bring it back at all. I don’t remember it taking damage, but I may have had my sound off at the time. I don’t want to impose, as this is very much your game, but maybe you could install an update that shows how much health your lights have? Maybe even a method of repairing them? (Also, this new world also has the same problem of enemies and bosses not appearing in the codex)
I tried looking for other causes for the beacon disappearing, but it seems to be an elusive bug.
I wasnt able to add a health bar or repair, but the codex should hopefully be fixed now.
I also noticed that the beacon was not allowing the beams to be extended anymore, and that should be fixed as well.
