Distinguished SOTW Technician
The entire instrument will be buffed to get it all to the same degree of shine and colour, so areas that are scratch free will still be buffed. If whoever doing the buffing has absolute understanding in what they're doing (using the correct mops and polishing compounds and the right amount of pressure while buffing) then they should be doing the least amount of harm (and Keilwerths have their engraving done and buffed over before lacquering so some of the definition has been lost anyway).Presumably if the engraved area is scratch free, then that part should not need buffing.
But if the company relaquering it has inexperienced polishers then there's the danger of them using the wrong (hard) mops with highly abrasive polishing compounds and too much pressure so the brass can be worn thin or have an uneven wavy look to it and the engraving will be lost in patches and pillars can get misaligned.
So it's best to see in advance examples of relacquer jobs done by a variety of companies offering this service to see how good their work is before handing your sax over to them as you may be very disappointed when you get it back. And if any serious harm is done, it's difficult to impossible to put right as you can't replace metal that's been buffed away and any successive attempts to rectify things will require more buffing and that means removing more and more metal each time.