The Wish Ender quest is a huge piece of garbage. There should be more checkpoints along the way, like one for every encounter in the first encounter, one at the doorway to the big hall after you get past The Descent, and add a rally point when you finally get the second orb over the edge with that stupid orb that I have to keep going to get because of all the ridiculous shadow Thrall.
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If you want a hand with it, send a DM. Bungie are decently reluctant to do anything with Shattered Thrones besides the things that will work - years ago they were asked to add rally flags and I believe the response I saw was it broke the encounters. So forcing in more checkpoint updates is unlikely.