If the piston is still in the bore at BDC and you hone from the top of the piston up, the area the piston is sitting in does not get cleaned/honed. Resulting in a step.Can you explain a bit more about the step mid-bore? My understanding of the flex-hone is that it doesn't remove appreciable material at all unless you spend hours hanging onto it. Maybe you are thinking of a bar hone?
Generically speaking, a used bore has the sharp edged of the original honing worn off, and the 'grooves' filling with glazing (fuel/oil/by-products). The 'glazing' and wear will go to the top/tdc of the barrel where the rings ride to the bottom/BDC. Honing restores the 'sharp edges' of the cross hatch. When run, again, the edges go away and the result is the bore above the piston is larger and a step results.
You must remove the piston and hone the entire barrel.
I often do not hone if the cross hatch is still visible and no marks on the barrel. A good scrubbing with a scotch brite and solvent.