it's not very very clear on how to downgrade your 3DS System and so on, I decided a guide should be created.
How to downgrade your 3DS to 4.X
I will be using my Pokemon X and Y Red 3DS that shipped originally with 6.1.0-12U.
1. Download the Gateway Ultra 3.0.1 Update from the Downloads Section on Gateway's website.
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2. Download the gateway.dg file specific to your region (In this case my region is U since I am in the US).
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3. Now download the MD5 Checker via this post (posted by the mod lemanuel) so we can check the MD5 of the gateway.dg file.
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4. Now open the MD5 Checker and Select the gateway.dg file by clicking add and navigating to where the file is located.
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5. After selecting the gateway.dg file and opening it, you should see the MD5 Checker display the name of the file, where it's located and the MD5. Go ahead and go to where the MD5 is and right click. Then compare MD5. You can paste in the MD5 for the gateway.dg file you downloaded from Gateway's website. If the MD5's match we can move on to the next step, if they don't I suggest making sure you downloaded the right file and re-dowloading the file it self.
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6. Now Backup your Nand to your Nintendo 3DS SDCard Via the Gateway launcher. You'll want to press a on "Backup System Nand" and "Start" to start the backup process. This will take about 5-15 minutes.
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5. Once you finish backing up your NAND, exit the gateway launcher and turn off your 3DS. Eject your SD Card from your 3DS. Now put your SD Card into your computer and open it up so you can view the folders and files. Make a copy your NAND.bin and put it on a safe place on your computer. Leave your original NAND.bin on there for now, we'll need it to be able to do the downgrade. Put the Launcher.dat from the Gateway Ultra 3.0.1 files on your SD Card along with the gateway.dg file.
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Note: The reason it shows up as Gateway EmuNand is I had formatted this SD Card for EmuNand. Doing a downgrade will not mess with your EmuNand. It also did not affect my save files.
6. Now make sure the LAUNCHER.dat, gateway.dg, and NAND.bin files are on your SD Card. Then eject it from the computer and put it back into the 3DS.
7. You will need a working internet connection set on your 3DS to do the next steps. Now boot your 3DS, open the web browser (found at the top of the bottom screen, a little blue world icon). Enter the URL go.gateway-3ds.com or prepare to open your bookmark and go to the go.gateway-3ds.com website. Turn your wireless communications on, go to the website and wait for the Gateway menu to boot. Then navigate to Downgrade Console at the end of the menu.
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8. Now press A on downgrade console and follow the instuctions onscreen. I'd suggest plugging in your 3DS to avoid any type of power problems as seen in my photo above.
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Thank You user StarKnight for providing the photos.
9. Allow Gateway program to do it's thing, this could take 5-10minutes, maybe less. When you finish you should be taken to the shutdown screen as seen in the photo, except it'll say software has closed. From there go ahead and choose power off.
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10. Now power on your 3DS. You should be back to one row like a normal 3DS fresh out of the box. BE SURE TO TURN OFF YOUR WIRELESS COMMUNICATIONS. Go ahead and head to System Settings and check your firmware.
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If you on 4.x then CONGRATULATIONS YOU DOWNGRADED YOUR NINTENDO 3DS SUCCESSFULLY!!!! Give yourself a pat on the back. If you aren't on 4.x then chances are you 3DS was probably bricked (Will boot to a black screen perhaps and not boot into the normal 3DS Menu). I can be of no help, sorry.
You may be wondering what's next?
You can delete gateway.dg off you SD Card but leave the LAUNCHER.dat as you will need that.
You can follow the tutorial for installing the gateway exploit and everything at this maxconsole post.
Enjoy your newly downgraded 3DS!
EDIT: , a sticky! Thank You!
EDIT 2: If you're using the EUR gateway.dg binary blob, you SHOULD format sysnand after you've successfully downgraded. This is due to an update nag that seems to appear. YES this would unlink your sysnand from your emunand, and you may find this rather bothersome, but it should get rid of the update nag.
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