Try this:
-Since the Flashcart's can not access the DSi-Mode yet(DSi Mode means using all the Hardware, the DSi can offer), and are only using DS Mode (They're using it only as a DS, which means parts are blocked and the flash memory stores other values than normal), weakly coded Applications do keep it in the bootloaders memory when being closed in an irregular way.Those Applications do basically use fast but insecure and instable read/write functions, but i won't go any further now, since most people that do read this Tutorial do only want to fix their DSi's.
Step 1) Make Sure you got the Error . Should look like this:
Step 2) Start your DSi and wait until the Battery is empty. (Having an empty Battery lowers the time to boot up . The Ds got two internal flash memorys that are both damaged when you have this error. With the low Battery the resetted one gets loaded while the other can't in the same speed)
Step 3) Remove the Bolts and extract the Battery for around 1.5 hours.Why we did this? All the Electricity needs to be out of the System to make sure it's only getting the Bootup Information from the Chip that got resetted and not from the other, if the other one could send it's information, we would still have the Error.
Step 4) Reinstall your Battery.
Step 5) You need to be fast now: Insert your Flashcard, and start your DSi.Start the Application you used the last time, before the Error appeared and close it legitly. In case off the SuperCard DSTWO SNES Emulator, just press the Exit Button. Other Flashcards like the R4i need to be soft resetted to the flashcard's menu, and need to boot up some game's rom.
Step 6) -Not Necessary but just feels a little more safe- Format your NDSi.
Step 7) Charge your Battery and enjoy playing your NDSi Systems again.
[http://forum.supercard.sc/viewthread.php?tid=7176|from here]