The way I understand it, fixing a card that has been fake killed can be a total pain. I copied this from the new DSTT card faq.
If your DSTT may have been destroyed by fake-killer firmware, try these steps:
1.Backup the files on your microSD card, and use the Panasonic formatter to reformat your microSD card:
http://gbatemp.net/index.php?download=4003
2.Grab the unofficial 1.17a02 (fake-killer disabled) menu from here:
http://gbatemp.net/index.php?download=6507
3.Copy the "TTMENU" folder and "TTMENU.DAT" file that are in the "English" folder to your microSD card.
4.Grab this archive:
http://gbatemp.net/index.php?download=4086
5.Copy "DsttFlashChecker.nds", "DsttFlashWriter.nds", and "DSTTDUMP.BIN" from the archive to your microSD card.
6.Make a folder named "games" on your microSD card. Copy 2 or 3 games (.nds files) to the new "games" folder.
7.Run "safely remove hardware", select your microSD reader in the list, and press STOP before removing your microSD card from your PC.
8.Insert your DSTT into the NDS. Insert your microSD card into the DSTT. Turn on the NDS.
9.Run the DsttFlashChecker program to see if you have a real or a fake DSTT. If you have a fake DSTT and suspect that it may have been destroyed by the official fake-killer firmware, run the DsttFlashWriter program to re-flash your DSTT. Note: if your flash cart was destroyed by the fake-killer firmware, it may take several tries before you can get it to boot up or run DsttFlashWriter. In some cases, it won't run at all, in which case you'll need to install "DsttFlashWriter.nds" and "DSTTDUMP.BIN" onto a working flash cart (it doesn't have to be a DSTT), run DsttFlashWriter and then remove the working flash cart and insert the killed DSTT before doing the restore (WARNING: if you don't switch them, you could potentially destroy your working flash cart).
10.You should be able to run your games now. You can delete "DsttFlashChecker.nds", "DsttFlashWriter.nds", and "DSTTDUMP.BIN" from your microSD card if you want.
11.Always keep the following in mind:
?Always leave some free space on your microSD card for save files and system files.
?Always put games into your "games" folder. Also, put homebrew into a folder. Leave as few files as possible on the root of your microSD card.
?Always use "safely remove hardware" to remove your microSD card from your PC.
?Use the Panasonic formatter if you ever have to reformat.
?Keep a backup of all the files that are on your microSD card. Backup your .sav files often.
?Make sure you don't use the official "TTMENU.DAT" (particularly if you have a fake) because it contains fake-killer code.
If the above doesn't work, you probably have a hardware problem. It could be your microSD card reader, your microSD card, or your DSTT. Try using a different microSD card reader. If that doesn't work, try a different microSD card. If that doesn't work, you should return your flash cart where you got it from. There is no good way to fix a contact or other hardware problem, but if you have a contact problem sometimes paper or cardboard inserted alongside the back of the DSTT can help push the DSTT towards the NDS contacts and can help them make better contact.
I just bolded the section I thought might help!