Does deleting the cache files in the USER directory hurt anything?
The user directory where the cache in question is:
Also is cycles what is generating this cache?
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Yes, cycles caches BVH (Bounding Volume Hierarchy) files in there when Cache BVH is enabled in Render settings > Performance:
Deleting them shouldn't do anything bad. Cycles will just regenerate these files (though it won't cache them if you disable Cache BVH), which might cause an increase in render times, depending on the complexity of your scene.