Flying with one working leg wasn't a problem. The issues started when Khan met new debris over the vast cavity connected to the underground graveyard, which he had spent some effort finding.
The sand was easy enough to deal with, but the other debris was annoying. The rocks and soil were still fine, but the metal shards shared the Nak's remains' fabric, so Khan's shockwave could affect them once he tuned it to that material.
In short, after a certain point, Khan was forced to dig by hand again, fighting against the pain and numbness radiated by his right leg. Crawling through the debris was even worse, but nothing sheer determination and many suppressed curses couldn't deal with.