Are you playing emulated, off a flashcart, or off a legitimate DScard?
If you are playing emulated, you should try replacing your .nds file (the .sav or .dsv files contain only data and therefore are compatible with any iteration of the .nds file). It's highly unlikely that it's your save file that is corrupted.
If you are playing on a flashcart, try upgrading your firmware for the system, upgrading your software, and replacing the .nds file. If the .nds file doesn't load, it could be because the anti-piracy is acting up (you need a patch for this). If that doesn't work, try backing up the .sav file on your computer and rebooting a recovery save from the flashcart menu.
If you are playing legitimately, there's little you can do, to be honest. Have you done anything to the game (e.g. Action Replay, glitches, etc.)?