After Crashing on Twilight Menu, All Apps Gone, except for one

Hiya all, need some help here

So I have some problems, nowadays I play ds games on my 3ds via twilight menu for nostalgia reason. At time, I put it on sleep (while still on playing ds game via twilight menu) because I want to do something else in meantime. Short story, when I want to play it again (about hours after I left it) the 3ds crashed.

When I boot it again, the apps that installed all gone, except the twilight menu itself. However, I checked on system app management, the installed games and apps is still listed there.
And I still can play the ds games on twilight menu without problem, though it is still crashing when I using button combo to return to twilight menu home or put it on sleep in some hours while still on (again).
So at first I think the sd card is corrupted/ can't be read properly but maybe I'm wrong since it can read the game on twilight menu.
Also I installed a theme, and it is gone too.

Anyone can help to restore the apps ?
I attached crash dump (I attached all of crash dump because the last edited date is all same) and screenshot showing my 3ds current condition. I'm sorry I don't have screenshot that show my 3ds normal condition

I appreciate the help. Thank you

 

Sorry,, I don't know how to type the crash dump in text.
If I'm counting correctly, it's about 60941 blocks. I'm using a 16 GB sd card btw.

 

sd:/roms/nds

 

Did you mean cia? or the installed game?

 

In folder games on root, but usually after installed games, I delete the cias

 

an

any solution to it?

 

Thanks for the info, I'll try it ..

And may I ask what made the problem arise? is it because the crash?