Saved worlds and data exist but are no longer seen by in game

I have several saved worlds and shaders/texture packs. They still exist in the file system and can be found by my file manager, however, minecraft no longer sees them. I even had to re-do my controls as it didn't remember my control configuration.

 

I have the storage location set to external so I can load worlds and back them up easier. This is still the setting in the app, I double checked.