3DS Titles disappeared from Home Menu

This issue does not affect anything installed as DSiWare, including TwilightMenu++ and games forwarded via nds-forwarder.

On the 3DS, Going to System Settings → Data Management results in...

Titles with gray X's on them:

install and run Faketik.

Titles appear listed normally, but still missing from Home Menu:

If this occurred after installing 300+ titles, delete some games form the Data Management screen until you’re under 300 titles.
If this occurred and you have less than 300 titles installed, use Chalanged's gm9 title fixer per their guide or go to the Nintendo Homebrew Discord and use the .tag missingtitles command. Follow along as instructed.

When the 3DS finds missing or corrupted data in the titles folder, it refuses to load the whole folder. the easy solution is to remove said missing or corrupted data. the hard part is finding the data. The gm9 script and the discord command do just that.  The file the bot asks you to upload, 'title.txt', is a list of all the files and folders in the titles folder. this allows the bot to  look for any folders that are missing files so you may delete them, which usually brings everything back. However, the title in question is presumably inaccessible and needs to be reinstalled.

Error Message asking to reset:

rebuild your Title Database.

A bunch of question marks or black boxes, or data management is empty and your theme is gone:

Your SD Card is likely corrupted. Backup the contents of your SD Card to a computer or phone, reformat the SD Card, then test its integrity.