Ah yes, the "trunk wiring harness breaks rear window" snag - for more information, see this post: Broken Sleeve on Electrical Harness leading to Trunk Lid - How to fix?.
Although I am loathe to ever criticize individual dealership service departments, I am beginning to think that perhaps the staff at your VW dealership are not especially familiar with Phaetons.
When you pick up your car - after the rear window and the trunk wiring harness have been replaced - be certain to function-check the following items before you even leave the dealership parking lot. All of these items can be, uh, 'screwed up' in the process of replacing either the back window or the trunk wiring harness:
Pertaining to the rear window replacement
1) Radio reception - both FM and AM.
2) Navigation System - make sure it picks up the satellites and determines the correct location of your car.
3) Rear window electric heat - put the car in the shade (out of the sun), start the engine, turn on the rear window defrost, then check the glass either with your hand or (far better) with an optical thermometer that the dealership can provide, to ensure the window heat is working correctly.
Pertaining to the trunk wiring harness replacement
1) Remote unlocking of trunk (from driver door switch) works
2) Remote unlocking of trunk (using key fob) works
3) If you have a power-lifting trunk lid, unlocking of trunk by pressing VW logo works.
4) If you have a power-lifting trunk lid, closing trunk lid by pressing button on lower edge of trunk lid works.
5) Start engine, turn on lights, check that all four red 'running' lights at the rear of the car work.
6) Place transmission in reverse, confirm both backup lights work.
7) Press on brake pedal, confirm that brake lights work (symmetrically).
8) Check that turn signals both sides work.
9) Ensure that there are no symbols in the display screen between the speedometer and tachometer indicating that bulbs are not operating.
Good luck with it all...
I do strongly recommend that you print out the contents of the discussion at this link: Broken Sleeve on Electrical Harness leading to Trunk Lid - How to fix? and give the document to your service manager before the dealership starts work on the trunk lid wiring harness replacement. Otherwise, given the batting average of your service department, they will probably install either the wrong wiring harness (there are two different part numbers), or, they will cross-wire the two identically coded wires in the harness, which will cause asymmetrical operation of the rear running lights.