I get simular DRO numbers once in a while, and just ignore the silly 0.0001" because it's meaningless from a practical point of view. If i do a reset, then i don't get say 3.999 instead 4.000 post jogging numerous times.
How do you really know that your loosing or gaining a single step?
IE: for a step per unit of 20304 on my lathe, 1 step=0.000049251"
To truly measure that you would need to be at some 400x with a calibrated microscope and no i would not trust the simple reverse movement of an indicator as i can prove that it's not indicating 0.0001" on reverse.
Not all steppers are created equal. Some are made better than others relative to how their poles line up and lock in at a postion ( which can be a silly 0.0001" of movement).
Just some thoughts on the matter,
RICH