I'd like to hear from you the way you perform the end play measurement (Thrust bearing axail clearance).
For big machines, machinists apply a large force (via jacks or other ways) to push shaft both sides and take the dial indicator readings. When the shaft is restricted by the thrust bearing, as the force is applied, the shaft can move a few thous more due to the elastic deformation of the rotor and bearing components. After the force is released the rotor usually retracts.
Of these two positions, which reading you consider?