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.