If you modify an alignment feature's theoretical values during execute mode, PC-DMIS changes the CAD to Parts alignment. This means that features in your measurement routine that come after the alignment, and are measured relative to the alignment features, shift by the amount of the changed theoretical values.
If you select the Ignore CAD to Part check box on the General tab in the Setup Options dialog box (Edit | Preferences | Setup), the CAD to Parts alignment does not change when your alignment feature theoretical values change. The features below the alignment are then measured in their same position. See "Ignore CAD to Part" in the "Setting Your Preferences" chapter.
You cannot use the Ignore CAD to Part functionality if you use Position dimensions in your measurement routine.
You can also control how PC-DMIS handles your features' nominal values when you update an alignment's theoretical values by using the UpdateBelowChangedAlignmentDuringExecution registry entry in the PC-DMIS Settings Editor. For additional information, see the "Modifying Registry Entries" appendix.