Once you have completed the installation of boot9strap and Luma3DS to your 3DS console, you no longer require the ntrboot exploit on a flashcart. To return the flashcart to its original functionality, simply restore the dumped backup using the following instructions. Before beginning, download the latest version of ntrboot_flasher.
Removing ntrboot from the R4i Gold 3DS
With the 3DS powered off, remove the MicroSD card from the console and insert it into your computer. Create a folder called ntrboot in the root folder of the MicroSD card. Unzip the flashcart backup archive and copy the resulting *.bin file to the ntrboot folder.
Navigate to the luma folder on the MicroSD card and create a folder called payloads and copy ntrboot_flasher.firm into it. Eject the MicroSD card and reinsert it into the 3DS console.
Insert the flashcart into the 3DS, hold the START button while powering on to boot into ntrboot_flasher. Follow the on-screen instructions to select the appropriate flashcart (R41 Gold 3DS) and restore the original flash. Once completed, press A to return to the main menu and B to power off the console.