After repeated testing of this, we have been unable to replicate any issues at this time. If you get a good example of it happening please send a ticket to [email protected] with your Debug.dat and example tune file for review.
The only difference between a write entire and write calibration is write entire writes the Strategy/Operating System+Calibration Data. Write Calibration does only the Calibration Data. Any changes you can make in VCM Editor effect only the Calibration Data, unless that change is in the Operating System section.