I was asked to do a somewhat similar task: have a flat pattern, with a hole pattern in it, and then form it to a complex surface. it was for a speaker grill.
Pro/E did not accurately form the hole pattern into the new complex shape. Rather it made the complex shape, and then projected the hole pattern onto it.
I don't know if this is relavant to your task, but it was interesting. Makes me less confident in flattening complex-shapes and getting an accurate hole pattern in the flat pattern.