Using a dividing head on a milling machine, it should not alter the balance. Furthermore this is a 3000 RPM diesel. The Cummins 12 valves are factory balanced with pistons within a gram and rod big ends within 10, but that's considerably closer than is even remotely necessary for a long happy life on a 3000 RPM engine that spends 95% of it's life below 2000.
These engine's don't see damaging harmonics until 4100 RPM and are rated for continuous 3750 RPM use at full rated load WITHOUT a harmonic balancer. The on the road engines have them to make owners happy, they're likely for looks more than anything in a stock or mild engine.
This particular engine already has 390,000 miles on it with very poor maintenance, fram filters and fueled to around 300HP since it was just a pup. It runs better than new, doesn't leak and if by some miracle it manages to come apart or start using oil in the next few hundred thousand miles I'll replace it with another $500 12 valve.