"Database Disk Image is Malformed"

Game version 1.21 and running the latest dev build 2.3.0 (had the same issue on 2.2.1 however)
honestly not sure what's causing this, but there are a few large chunk holes, and when I move to the area to load them, my disk & CPU usage spike for ~30 seconds, and then after the usage goes down, when i move away the holes reappear.
My CPU is running at a constant 70% even when idling, which is unusual. Turning down LOD builder threads does nothing for CPU performance, but turning file handler threads down instantly drops it.
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