In a sentence.
To get the bottom of that area flat, flat as the proverbial pancake, displace it a very little lower, add a plane object, move the plane to the 'caves' XZ coordinates, scale the plane's length A/Length B settings enough to cover the hole then, just lower the plane to the desired level of the bottom of your pit, make the plane just slightly wider than the hole to save unwanted sub-terranean render time.