I assume you have the same number of spokes on both hubs. Did you discuss what would be required for the changeover before dropping off the rims? Before modifications were attempted? Did the wheel builder discover problems during the build, then inform you before destroying your rim? And, have you seen it?

Are the hub flanges for the two powertap hubs different diameters? Different spacing? 10s vs 11s? If the nipples are at the aluminium outer rim, then go through a deep covering, then out a second small hole, then the configuration would be very sensitive to flange diameter, and maybe even flange spacing.

I am surprised that a regular bike shop would have professional equipment and expertise to attempt modification of deep wall CF rims.

I am just a little surprised they would even attempt the job.

If it is non structural CF fairing that has broken, can it be repaired? Maybe someone local has some CF repair experience. You could contact Calfee. It says they frequently reject rims and carbon/aluminum bonded joints, but it doesn't say they always reject them.

Anyway, if the shop communicated the difficulties before and/or during the process, and you authorized them to go ahead, then I would expect you to take full liability.

On the other hand, if you dropped off the wheels without a hint of potential issues, and the first you heard from them was after the rim was damaged, then I would expect them to take at least partial liability. But, that would still depend on whether it was something the wheel builder did, or a previously undiscovered flaw in the rim.