Hiii! I'm so sorry you encountered so many issues!:(
Once you get to the point where you have 3 companions and one light left, you can still use it to light up the memorial you,re talking about which will unlock some pilars you'll be able to jump on to continue your journey! Your light will come back to you once you complete it, as you only permanently loose them when you give them to a companion. I also would recommend to not leave one light in a door when it needs two of them to open cause if you do that the light will get stuck there as long as you dont throw the second one in. We didn't encounter this issue before so we couldn't fix it on the build, really sorry! Hope this helps and don't hesitate if you need more details!
(Also thank you so much for your comment and for playinnnggg<3)