https://en.wikipedia.org/wiki/Philosophical_zombie

A philosophical zombie (or "p-zombie") is a being in a thought experiment in the philosophy of mind that is physically identical to a normal human being but does not have conscious experience.

I think that it is covered by "atom-by-atom". I suppose all matter that enters the machine is moved (or even if copied). Heart will just kickstart, because it runs on electrochemistry, if the ionic energy is there from all required "atoms". But that raises the question: does the energy state of that matter get transfered?

And what would kickstart your heart beating?

Skydive naked from an aeroplane, or perhaps a lady with a body from outer space

Maybe just a custom built bike doing 103

The heart never stops beating. It's created somewhere in its natural cycle and just continues doing what its molecular and electrical state dictate it does.