If that's the case you might be able to restore your files, I'm terrible at explaining things though.
If you are sure you injected the emunand and you have the content from that emunand on the SD card, check the Nintendo 3DS folder, you should find folders with random letters and numbers (one for each console the SD has been used, in most cases its two, one for Sysnand and other for Emunand). What you have to do is go into the EmuNAND folder (In most cases, it's the folder with the biggest size in it, assuming your Sysnand is empty). If what happened to you is what I think, then you should have two folders inside (with random letters and numbers again), one of them is the one with all your files and saves (hence the biggest of the two), and the other one should be the folder that the Emunand is currently accessing, move all the files inside the folder with your stuff to the other folder.
It might not be what happened to you, but this way I managed to recover a friend's emunand. Good luck.