New 3DS XL - just modded and already issue

Hi everyone, i just homebrewed my first 3ds xl today. First was everything fine all apps (FBI, hshop, etc.) worked perfectly. Then, suddenly the 3ds crashed and restarted. After restard all homebrew apps and games dissappeared. In settings at data manager i can see the games are still installed. Even when i plug the sd card in to a computer all folders and files are just there correctly. What could the issue be?

Edit: I just changed the SD Card and copied all files to a fresh new formatted one. Still same issue. Apps and games do not appear on homescreen. My gilrfriend also created a folder to sort system apps, maybe she did something like hide the other apps, unknowing?