walkerlrcs,
I presume this is a Slab-On-Grade and UNbonded post-tensioning was used.
Your contractor needs to be mindful of the tendons and their anchorages - do NOT chip too deep within the slab depth, NOR too close to any PT anchorages.
As "ishvaaag" indicated, there are repair materials available today that will restore the concrete to near what it was be before.
I would chase the slab parallel-to, but offset-from, the preferred conduit location and the actual tendon/s location/s. You should have a good knowledge of the tendon locations since this is a new pour. And if the slab edge is exposed you can check the tendon locations via the grout plug. Where the receptical box is going make sure that this is not at a tendon or tendon intersection location.
Make sure that the person who does the chipping is not the lowest paid laborer - if he/she chips too deep or too close to a tendon that may produce further problems. Good supervision is recommended. I would minimize the use of water during the chipping - and at tendon intersection locations that the laborer does a bit of "needle work" on the chipping to ensure that the cross-over tendon is not hit.
Re long-term effects - provided that caution is taken with the actual chasing (the extruded sheath is not exposed, nor water is introduced into the chase) and the repair material is selected and installed correctly i would see no long term detrimental effects.
I would recommend a prebagged product for the repair and not a site mixed or mason's mix material. Pre-bagged materials are easier to site batch.
I would keep the chase as shallow as possible, and it may be worth considering a 2 component epoxy as the repair material - probably mixed with a dry silica sand. For very thin and long patches cementitious materials can be problematic.
I would be documenting all aspects of the chipping, chasing and install - with photographs - i would also consider that this aspect of work should carry a longer warranty period - the contractor made a mistake and an increased warranty period is not unreasonable.
HTH