Actually, the same happened to me just a few hours ago, I was installing a9lh to a friend, after I used Emunand9 to wipe the Emunand partition, after that Luma didn't boot anymore past the config. screen. Actually pressing start to save the config freeze'd the screen, but the payloads worked fine, I updated the a9lh payloads (Plailect guides links to the old payloads) and the console turned fine without the SD card. Thinking it was Luma the problem I downgraded to Luma 5.5 and it booted correctly.
I dunno what could have been the problem, but if somebody else had the same problem then maybe Luma >6.0 might have some bugs that prevents booting in some consoles, if it helps, the console was a USA o3DS on 11.0. Latest Luma works fine on my n3DS by the way.