Remove Intersections will remove any points at the junction of three or more edges. If this step was already performed during Sim Clean, it will make no difference here.

<aside> ☠️ Intersections must be removed, either here or during Sim Clean, otherwise it is impossible to determine correct bone chains and directions. However, if wished, you can disable ‘Remove Intersections’ during both Sim Clean and Edge-2-Bone but the results will not be clean.

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With Remove Intersections enabled

With Remove Intersections disabled