For your disappearing river, how about a geological sequence of flat land w/ curvy river, uplift to become plateau, steep canyons cut during the uplift, then earthquakes somewhat crumble the canyon, climate dries up some, dunes drift over the former canyon lands. Result being a sea of dunes (and rocky outcrops if you like) with a nice roomy former river course beneath.

The sand might at first tend to filter down and clog the cracks between boulders - just assume the clogged bits could get washed back clear by occasional high flow. That could be a silly assumption, but who's going to be down there inspecting your geology? :-)