ok, so it looks like the encryption keys have changed since you've done a system format.
first you will need an empty / blank SD card that is 4gb or bigger.
1. Insert your current 3DS SD card into your computer, copy these files to a folder: 'luma' (folder) and 'arm9loaderhax.bin'
2. Insert your blank SD card into your computer using a card reader. Copy the 'luma' (folder) and 'arm9loaderhax.bin' to this SD card.
3. Download EmuNAND9 - (Main Topic here: http://gbatemp.net/threads/release-emunand9-open-source-emunand-formatter-manager.405921/
Download version '20160812' from: https://github.com/d0k3/EmuNAND9/releases
Also download Decrypt9WIP if you don't have it: https://github.com/d0k3/Decrypt9WIP/releases/
Get the 'Decrypt9WIP.bin' copy it to your luma payloads folder and name it "up_Decrypt9.bin"
Get the EMUNAND9.bin file from the zip, copy it into the 'SD:\luma\payloads\' folder and rename it to 'down_emunand9.bin'
4. Copy EVERYTHING on this new SD card to a folder on your computer the SD card will be formatted in the next step.
5. Take out your SD card, put it in your 3DS, hold the 'down' button on the d-pad and turn on the 3DS, you should boot into Emunand9.
6. choose 'SD Format Options', select 'Format SD (EMUNAND Default)
7. This will format your SD card with an EmuNAND partition, once done, press 'Select' to unmount your SD.
8. insert your SD into your computer, copy the sysnand.bin file to the SD card.
9. Choose 'EmuNAND Manager Options', select 'restore file to 'RedNAND'
10. Select your 'sysnand.bin' file and restore it to your EmuNAND, once done shutdown your 3DS with 'dpad-left + start button'
11. Put the SD card back into your computer, re-copy the 'luma' folder and the 'arm9loaderhax.bin' files to the SD card and reinsert the SD card into your 3DS.
12. Hold the 'R' trigger button while you turn on your 3DS, it should boot Luma 3DS and start your Emunand (which is your old sysnand).
(If it doesn't boot, hold select to access Luma3DS config, untick 'autoboot sysnand' and untick 'sysnand is updated' then try booting luma normally)
Now you have an emunand, does it have FBI (or another CIA installer) installed to it? (I'll guess no, as it was your old sysNAND)
if not, you'll need to inject FBI into health and safety app.:
1. Download: UniversalInjectGen_v0.3.zip from this post below:
you'll also need the CIA of FBI from: https://github.com/Steveice10/FBI/releases/
2. Start Decrypt9, choose EmuNAND options, choose 'Miscellaneous...' then 'Health and Safety Dump'
3. Dump to the filename hs.app then press 'Select' to unmount the SD card,. put the SD card back into your computer.
4. Extract 'UniversalInjectGen_v0.3.zip', copy the hs.app from your SD card and your downloaded FBI.cia to the 'input' folder
5. Double click go.bat, once done, copy 'FBI_inject_with_banner.app' to your SD card.
6. copy the CIA of 'Tomodachi Life' and the CIA of JKSM (JK's Save Manage) to your SD card.
You can get 'JKSM from here: http://gbatemp.net/threads/release-jks-savemanager-homebrew-cia-save-manager.413143/
The download link is in the spoilers under the QR Codes/DL Links.
Make sure you have at least 512 megabytes of free space on your SD card, if you need some space, you can
remove the sysnand.bin if its still on the SD card, its already been restored, so you don't need it anymore.
7. Insert your SD card back into your 3DS, press 'B' to remount the SD card.
8. in Decrypt9, Choose 'EmuNAND options, then 'Miscellaneous...' then 'Health and Safety Inject'
9. select the 'FBI_inject_with_banner.app' and inject it into your EmuNAND.
10. press 'start' to reboot your 3DS and boot into emunand.
Now you have FBI setup on your emuNAND.
Now to install and get your save data.
1. Start Health and Safety (Which should be FBI instead)
2. Install your 'Tomodachi Life' CIA using FBI.
3. you will also need to install JKSV (JK's save Manager).
4. Once they are both installed, start 'Tomodachi life' and let it make savedata.
5. Shutdown your 3DS and take out the SD card.
6. Copy the 'Tomodachi Life' save data folder (00008c400) to your SD:\<id0>\<id1>\extdata\00000000\
7. Start FBI, go to Titles, find 'Tomodachi Life', select it, and delete the secure value.
8. start 'Tomodachi Life' game, hopefully your saves are still there.
9. if so, start JKSV,from the main menu, select 'SD/CIA' then select 'Tomodachi Life' then choose 'Export ExtData'
10. Decrypted saves will be exported to SD:\JKSV\ExtData\
11. Insert your SD back into your computer, copy the decrypted save folder to somewhere safe.
12. you can now switch back to your current SD card that boots sysnand, copy the Decrypted saves back to JKSV\ExtData folder.
13. Insert the original SD card that boots sysnand, start JKSV and select SD/CIA, select 'Tomodachi Life' then import ExtData.
14. Start the game and check that your saves are there, if so, shutdown your 3DS.
15. insert the SD with the EmuNAND partition on it and start EmuNAND9 (hold 'down' on the d-pad on boot)
16. choose SD Format options, choose 'Format SD (No EmuNAND) to remove the EmuNAND partition
17. let it format, hold 'left' on the d-pad and press 'Start' to poweroff.
18. Swap the SD card to the one you use to boot luma and sysNAND.
19. phew.. all done.. (hopefully it all worked and you have your saves back)