My save file shows up just fine, so I have no idea why yours won't... The only thing I find disturbing is the fact that the DSTWO's EOS keeps saying the last saved date of nearly all of my save files is 00:00 1980/00/00, but I've seen that on multiple other OS's, so I won't worry about it.
Still though, your problem is incredibly weird. Have you perhaps tried performing a search through your entire microSD card's content to find out if it is maybe moved to another folder accidentally and the DSTWO can still read it?
Or, it could just be like 9th_Sage already said, that you're looking in the wrong folder (I've heard of other flashcards putting save files on the root of the card, so you're possibly looking there where no saves are to be found).