Modifying Phase information will only affect New Projects.
You can update an existing project to reflect the the new Phase Information. from within the Project see D-Tools> Options > Phases > Reset Default
As for Calibration, etc., if the fully burdened labor rates are the same as say the "Finish" phase and no equipment is involved, you may consider just creating a Labor SKU. This SKU could be added to the Package that includes the equipment that requires Calibration. There are many ways to approach this. The SI 5 documentation gives a lot more information related to Phases. Since the concepts are the same for Both SI 4 and SI 5, I would suggest that you download the docs and review.
See the User Guide
SI 5 Documentation
Also define your business process and then set up SI to support those processes. You may not require a Finish and Trim phase. However you may require Phases we do not suggest. Do not attemptto bend your business to fit the D-Tools settings.