New Nintendo 3DS/Nintendo 3DS 2015(not XL) can't detect microSD Card

I own a New Nintendo 3DS/3DS 2015 (not XL), So I made a flipnote using Flipnote Studio 3D, I wanted to copy the flipnote to my phone, so I put the 3DS’s microSD card in my phone and copied the files there. (I also put my phone's microSD card in the 3DS and the 3DS could read the microSD card if that helps.)

After that, I put the 3ds’s microSD card back in the 3ds and my games and apps and other stuff were gone, I checked data management in settings and it said “Could not detect a microSD card".

Help