Titles not appearing on home menu but appear in software:
Take SD card out of 3DS, put in computer and scan and fix it, put it back into 3DS, your welcome.
Some games not loading past title screens/corrupted save data across multiple games:
reformat SD card with a tool like DiskGenius (MAKE SURE YOU BACKUP YOUR DATA!!! PLEASE!!!)
Titles can't update on the home menu:
update them through hshop.
Screen Yellowing:
Configure the screen filtering.
Virtual console games added through cow instead of downloaded as an official Nintendo virtual console release not saving:
Either use an emulator or just download actual virtual console games.
If you are encountering any other issues feel free to comment them on this thread and I will try to help you find a solution.

 

[ChronoCrossfangirl2002]

Titles not appearing on home menu but appear in software:
Take SD card out of 3DS, put in computer and scan and fix it, put it back into 3DS, your welcome.
Some games not loading past title screens/corrupted save data across multiple games:
reformat SD card (MAKE SURE YOU BACKUP YOUR DATA!!! PLEASE!!!)
Titles can't update on the home menu:
update them through hshop.
Screen Yellowing:
Configure the screen filtering.
Virtual console games added through cow instead of downloaded as an official Nintendo virtual console release not saving:
Either use an emulator or just download actual virtual console games.
If you are encountering any other issues feel free to comment them on this thread and I will try to help you find a solution.

Shouldn't you specify what tool to format it with? As Rufus can be a bit wonky with the 3DS for some reason, also allocation size matters but
it all depends on what size SD card you have.

 

[Ay4nami]

Shouldn't you specify what tool to format it with? As Rufus can be a bit wonky with the 3DS for some reason, also allocation size matters but
it all depends on what size SD card you have.

yep, i just edited it.

 

[User154]

Great guide but just a couple of things I would add/amend.

If problems are arising from the SD card, roadkil's unstoppable copier is great for backing it up, most people's preffered tool for formatting is guiformat (Might also be worth mentioning the SD card must be formatted as FAT32). Also, after formatting, but before transferring your data back to the card you should probably be checking it with h2testw

Lastly, and if this has changed I welcome being corrected, but I believe mentioning that app for updating titles is against the forum's ToS, as it used for distributing warez.