I am unable to tether the cubes in the Blooming Deep lost sector. Tried with all three characters. Ran additional Alone in the Dark quests to see if it would let me progress. I can see the ghost flying around but there is no resonant energy on the cubes and they won't activate when shot. I am now stuck at 8/11 geometries.
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There is a commune spot near the red cube you need to interact with first. Head to the spot where you can see both of them (there will be a prismatic pool on the ground), if you keep going past the prismatic pool you'll see a tight gap you can walk through that lets you behind the red cube, you'll find the commune spot there.