Within the OnecncXR environment, I guess I would see a couple of ways around that problem: simulation of the program/process, and hole feature recognition. OneCNC's feature recognition will detect complete arcs as potential holes to be drilled (and all visible points as potential hole centers), and list them in a tabulated form which shows their diameters, and the quantity of holes of a given diameter. The layers are irrelevant.
I know it doesn't help you solve the problems in your own situation, but I thought that you might want to know about it. It could sure reduce the liklihood of spoiling a part.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)