While I haven't updated Super Smash Bros 3DS since Version 1.0.3, I've been debating updating it to the latest version of 1.0.5.
However, I've heard that version 1.0.4 added an extra update to the game, which is done once you start up the game after the update. I vaguely remember reading about it when it came out, that if you delete the game data then start it up without it being there, your save file you have won't be able to load. If I recall correctly though, you can carry on from this point with a fresh new file.
When you re-update Smash Bros 3DS back to the most recent version, does this give you back your original file that you had before removing the update data or the newer file in its place? I assume the same will be applied to when the DLC is out.