Here is an alternative to "Cut" and "Voxel Subtract" that leaves your meshes geometry intact and just squashes the mesh to fit a cutter.
You just add the cutter as a child, select the parent and "Mesh/Fit to.../Child Objects (Cutter)".
The cut surface is left selected for easy smoothing etc. Below I use "Smooth Mask", "Mask/Bell" and "Mesh/Smooth" to even out the edges.