Today I decided to try and finish up the final pieces of the Inquisition of the Damned lore book and also the last dead Ghost (Omar Agah's). Previously I had obtained the lore near the very start of the dungeon but had never completed the first part of the dungeon so I still have 4 left to acquire. I watched a Youtube video showing the locations of the pieces I still needed so I went into the Pit. After completing the first challenge I proceeded down the stairs and jumped up to the area above where IX.X Aprocrypha - Consequence of Sin should be, but it wasn't there. I decided to proceed. I entered the Ogre tunnels and located Ogar's Ghost and finished that (finally). However, the other two lore pieces in the tunnels also aren't there: IX.X.II Apocrypha - Thy Song Shall Become Death and XI.X Apocrypha - To Forge An Anvil.
At this point I gave up and didn't even try to see if the last piece would be visible.
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Same, I was helping a buddy get Xenophage and get his first PoH done at the same time. So, I went to get him the lore as well. But, none of them were there.
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I imagine it’s the same issue as ahamkara bones being missing from Shattered Throne which they’re apparently “investigating” so who knows