Emergency stop removes power from your steppers, I believe, so when power is restored after a reset, all the steppers do a thump as they line up with their nearest step. I got used to it, and try to use soft limits, so I never need emergency stop.
Why do you need to reset. Put a M30 at the end of your program, or use the rewind button. You can hit program stop (Escape) at any time, then manually retract Z, hit rewind. And restart your program - no clunks except at initial power-up. Even changing programs does not require reset. Just Hit STOP.
It sounds worse than it is I think. Just 3 or more strong steppers jumping half a step or so to line up with the nearest pole.
Make sure the couplings to the stepper motors are well secured against slippage.