No, the sugars won't "go" anywhere. The wort could carmelize a bit if the boil was exceedingly too hot and thick (like when you make hard candy, the temperature goes up over 300) but I can't imagine that happening in regular wort as there aren't enough sugars to raise the boiling temperature over 212, no matter how powerful the element is.
I'd check the preboil gravity and see where the low efficiency is coming from. It could be from conversion (check for conversion with iodine), a poor crush, lautering inefficiently, etc.
If he's starting with 8 gallons, it could be something very simple like oversparging to get that much wort. The last runnings could be very low in gravity- have him check that first!