Which are we going with on how it works? You’re perfectly reconstructed or something else that allows the other Star Trek plot lines? In the prior case yes, in the latter it would depend on how it does actually work.

If it is supposed to re assemble then the only explanation I can come up with is that each atom is getting actually duplicated in some sci fi Schrodinger’s non collapsing super position and both are authentically the original atom. That’s not a ship of Theseus situation though since your replacing the ship parts with the original ship parts.

That is so sad Deponia is so good though. They just bit off more than they can chew