

The pathfinder tool will still mess with the shape stacking order, but this way it will be irrelevant because the two shapes being shuffled around are both ultimately in the part of the stacking order that the pathfinder result will occupy. Paste shape A directly in front of shape C in the layer order (Copy Shape A, select Shape C, select past in front /CMD+F) - then perform the transform.

*A is no longer in present as the Minus Front tool causes the shape you are cutting out with to disappear.

(furthest forward) Shape C - (furthest forward) - Shape that you have created by removing shape A* Then the pathfinder tool will cause 'Shape C - (the shape being cut into)' to jump forward to wherever in the layer order 'Shape A - (the shape doing the cutting)' was. (furthest back) Shape C - Shape that you are wanting to alter/remove Shape A from (furthest forward) Shape A - Shape that you are wanting to remove from Shape C Intersect: Intersect creates a new shape where the other 2 shapes overlap. The problem is that if the object/layer stacking order is this: Minus Front: Minus Front cuts out the bottom shape where the front shape overlaps it.
