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Can changing master probes cause issues?

Yearly calibration tech was just in and needed to use a "service" probe, a longer probe for extra reach in their calibrations.

Now we're having issues qualifying the probes after running in house calibration.
First time only the master was checking small, so we re-ran calibration.
Now all the probes are checking the Ø of the sphere .0002"-.0004" small.

We answered Yes to 1st probe, No to the rest for the has the sphere moved question.
We have reset to theoretical box checked.
STD Dev results are looking good.

Shouldn't answering yes to has the sphere moved and resetting theo's for the master probe override any old info?
We had this issue on both CMMS.