As @parachvte mentioned above, the Z offset that you change while the print is running is only kept for the current print. The Z calibration that is set at the end of the 3 x 3 matrix is saved. I have heard many people say that their calibration has not been consistent from one print to another meaning the print right after a successful print.
What I have been doing is bump the Z offset up a couple of .05mm’s worth at the very begining and then while the skirt is printing, bump it back down as needed. Sometimes I have to bump it up even more. You can kind of get a feel by looking at it whether is is squishing down too much or not squishing down at all. Sometime it doesn’t even contact the bed so I have to bump it down a number of clicks.