Offline Programming - resetting to nominal

This is a large topic and I am only asking a couple of questions that I have come up with over the years....

I program almost all of my programs offline and upload the programs to a directory. The program are then opened from this directory for use on the CMM. If there happens to be a problem with the programs I then open them again on the offline system to troubleshoot. This is where MANY of the questions come from. Perhaps I need a logic upgrade but my current logic says that a program that is created from a model, from which all alignment and feature nominal data is generated, should then return nominal measurements when the program is executed offline again. It does not. In fact, there are times when the features are not even located on the part anymore. They are out in space somewhere.

I will stop there before I get to far from the main question: which would be.... What would cause the nominal information to change so much? How can you keep this from happening? How can you return the program to the original nominal without having to regenerate everything?

Thank you,

Peruzzi