Megachiroptera and Microchiroptera are no longer valid taxonomic clades. Molecular evidence has restructured the order into two suborders, the Yinpterochiroptera and Yangochiroptera. Megabats now belong to the Yinpterochiroptera, accompanied by some of the bats formerly known as Microbats.
It is suspected that certain bats lost the ability to echo locate, as opposed to it evolving twice in separate lineages, but to the best of my knowledge, it is not fully resolved yet.
Great article, Bats are awesome. They can teach us a lot about healthy aging.

Reference for phylogeny: http://science.sciencemag.org/content/307/5709/580.long