I've been experiencing this myself as of now. I've been trying to make a custom theme with sound effects/bgm and once I "install" I'm prompted that same message you got. Do exactly what you did by taking out the SD card and powering up the system. After that insert the SD card into your 3DS and...
@K3Nv2 I got some cheapies at wallys, that are pretty good, already have lost a few expensive ones (one falls out and gone, can't find) while cutting grass so bought some cheap ones, and of course never lose these cheap ones. (Cheap meaning only $35, compared to air buds which I only have 1 of 2 now)