As far as I know, z height affects all layers. Check out https://forum.prusa3d.com/forum/original-prusa-i3-mk3s-mk3-how-do-i-print-this-printing-help/rough-top-layer-surface-on-new-prints-after-recent-z-axis-calibration/ and see if that makes any sense.
This has happened to me before - a messed up z height will affect all layers because the squish isn't there at any layer. You'll always have that difference in height between the surface being built and the nozzle no matter what layer you're on.
