how to add vertices to a mesh and showing changes

I have been racking my brains for days now, searching everywhere i can think of to find some answers but i cant seem to figure it out. im toying with the idea of a mining simulator where the 'cutting drum' of the miner actually removes terrain. so far to do this i have a cylinder (a rigidbody) with a slightly bigger cylinder(just a trigger) as its child. the cylinder drops (thru gravity) onto a cube... to simulate the cutting drum hitting the terrain. upon the collision, all of the vertices of the child cylinder which overlap into the bounds of the cubes collider are added to an array, the vertices of the cube are then also added to the array and the cube is fed the new data so its mesh can include the extra vertices from the overlap. my intention being to reshape the cubes mesh to now have an indent where the cylinder struck it... and to eventually allow the cylinder to drop completely through the cube by basically building a hole in it.

The reason i am trying to do it this way is so that i can 'attack' some terrain with a mining machine and actually make my way underground (burrow into the mesh) and cut out roadways with its cutting disk.

i simply cant get it to work. the mesh becomes kind of fractured looking after recalculating norms. any help would be very appreciated (sorry this is so wordy)