Ok so my problem was solved guys just thought I'd let you know how I did it. Again, happened completely randomly which was very odd. I replaced the A9lh bin file (even though I'm not on A9lh the bin file is good to have on SD anyway apparently so put a fresh one in), copied over luma 3ds v 6.6 replacing the boot 3ds x files. Redid the initial configuration settings ticking 'show Nand in user string settings'. Now loads up as it used to. If you have a random similar glitch then this may sort you out.