My 3DS needs doesn't acknowledge when a game is taken out

Something strange has happened with my 3DS: any time I want to switch the game that I'm playing I have to take the game out of the system, select the game on the menu again and have my 3DS tell me that the game isn't in the system anymore before I can put in a new game and play that. This all started when I put my SD card into my Laptop in order to see if I could transfer some pictures from my 3DS. After that the problem started. It stopped after a while but as a cost my Pokémon Alpha Sapphire save data was corrupted. That was about a month ago. I recently tried putting Alpha Sapphire back in my 3DS to see if it would miraculously start working again (it didn't). I cut my losses and decided to play some Phoenix Wright. Just now I decided to switch to A Link Between Worlds and I noticed the problem had come back. I don't want to lose anymore save data. How can I fix this problem with my 3DS without having to restart a game?

P.S. if anybody happens to know of a way to regain my lost Pokémon data and could tell me that would be appreciated as well.