Accuracy in Pro/E is a little different than you would think. What it means when you say a part is at .0012 (default) is that it is comparing the overall envelope of the part to the smallest edge on the model. Useless I know. It means nothing. We (the users) *****ed at PTC back in the early 90's about this and the solution they came up with is "Absolute" accuracy. Think of it as "regardless of feature size". There is a .mfg file and a .asm file used in Pro/NC, go to the .asm file and select "edit" "setup" "accuracy" press escape and select absolute. It will ask you to "enter a value" or "select a model". Press "select a model" and select your reference part (the part you are machining). Select ok to regen the assembly. You have to do the same with the workpiece, once again selecting your reference model. What this does is say "I don't care how big my part envelope is, set my accuracy to xxx" Hope this helps.
Modeling in Pro/E since 1991