I assume the energy (heat) from the atoms being slowed down is transferred to the laser photons. Where does it go from there?

the photons are absorbed by the atoms.
they are traveling toward each other , so when the atom
absorbs the photon the momentum of the photon slows the atom.

look at the video at 3:30 from the begining.

or click this link to go to the moment.

3/4 inch of dust build up on the moon in 4.527 billion years,LOL and QM is fantasy science.