did you add some games on your microsd after playing?
i also had the same issue, but only when i remove the SD card out of sky3ds+ after playing.
the thing is, you have to press any button at sky3ds+ (also known as switching games) before ejecting->pulling the sd card out of the sky3ds+.
because... well im not really sure about this, but some games were saved in SD card(inside 3ds), and you have to switch games before shutting down 3ds to copy the save from SD card(inside 3ds) into sd card in sky3ds+.
basically you have to save the save after saving.. O_O
No, you don't have to on Sky3DS+.
