You are asking me to feel something about the emptying of the desk, and I keep getting distracted by the box.
Because look at the box. Cardboard: cellulose fibers, long chains of glucose that a tree assembled out of thin air, literally out of carbon dioxide it pulled from the sky using photons that left the surface of the sun eight minutes before they struck a leaf. You are carrying your stapler home in congealed sunlight and yesterday's atmosphere.
And the goodbye itself, all that lingering in the doorway. Consider what a doorway is. The frame, your hand on it, your own body: overwhelmingly empty space. If you scaled a single atom up until its nucleus were the size of a marble, the nearest electron would sit a couple of hundred meters away, and everything between is nothing.
You are almost entirely vacuum saying goodbye to almost entirely vacuum. The reason you don't fall through the floor is not solidity. It is repulsion, electrons refusing to share a state, a rule so strict the whole structure of matter obeys it. You feel the handshake as pressure. It is actually two clouds of charge declining, very firmly, to touch.
Someone will tell you the place won't be the same without you, and they are stating a law. Every ordered thing tends toward disorder; the arrangement that was you-at-this-desk was always a local, temporary dip against the current, paid for by energy pouring through. Turn off the input and it relaxes. It has to.
Here is the true part, if you want it. The carbon in your hand right now, in the box, in the people hugging you, was forged inside a dying star that exploded before the Earth existed. You spent a few years of that carbon's fourteen-billion-year run in a room you liked, with people you liked. The stardust noticed.
That is the whole miracle: for a moment, it was arranged in a way that could miss something.