Section V of
3ds.hacks.guide/installing-boot9strap-(ntrboot) won't work on a DSi. This is the 3ds guide.
You need temporary access to 2|3DS console with CFW (or – on stock 2|3DS – simply ntrboot into "ntrboot_flasher". If this does not work, ntrboot into GodMode9 and chainload the flasher.) You will need to find a copy of the flashcart firmware/flashrom online. There are magnet links for downloading them via torrent on the guide.
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Another possibility – depending on your flashcart – is starting it's official firmware updater/flasher (if available).
Starting the official flasher can be done:
- With another flashcart on DS-(Lite|Phat) by hotswapping the cart after loading the updater/flasher.
- Maybe with homebrew on DSi (unlaunch, TWiLight Menu++ → ).
- Another possibility is accepting the loss and switching to using TWiLight Menu++ instead of the flashcart.
- Edit: This is not a complete loss of course. The thing is still very helpful for 2|3DS consoles and can likely be restored if you ever decide to buy one.
- Maybe with "Download Play" by uploading the .nds file from a Wii with Homebrew Channel → I successfully tried this method for R4i Gold 3DS (r4ids.cn) on a DS-Lite.
Edit 2:
Just for sake of completeness: Deleting any data will not help.