Done all that still no luck sadly
The "oh shit, this is bad" extended guide.
Before we continue your journey to restore your o3DS, there are several prerequisites that should be met.
I - Make a one-to-one copy of your SD card setup and put this somewhere on your computer or external pen drive. This for insurance that you call fallback on retrieving anything of importance that you might have missed in your rebuilt setup.
II - From step 6 above, verify all your game saves and extdata were backed up in their
Checkpoint or
JKSV folder. Set these safely aside on your computer separate from the "insurance" backup.
III - If you have GBA Virtual Console games, you'll use GodMode9 to backup their saves. Edit - You might need to use *.3dsx FBI to launch them in the
Titles listing.
IV - Your custom firmware is using Luma3DS v9.1, GodMode9 v1.7.1, and boot9strap v1.3 on both your SD card and CTRNAND. Power the o3DS in two separate sessions: with card and without it. Verify the versions of Luma3DS and GodMode9 in (Start) and (Select) boots. For information about updating your custom firmware, check these:
-or- for a condensed, combined guide of the above two:
V - Unless you already have *.cia or *.3ds copies of your games saved somewhere, you will need to resort to redownloading your collection at places like
that iso site. Although not recommended, you may backup all your installed games, DLCs, and updates into *.cia:
There is a possibility some of your current titles are corrupt. Unless you have very hard to find games, it's better to start fresh.
VI - You are positively 100% sure without a doubt that you do NOT have ~300 3DS titles and/or 40 DSiWare titles installed on HOME Menu. If you have 300 3DS games or 40 DSiWare games, your icons will disappear.
[WIP, will be continued in next post]