You guys have forgotten, 9.2 CTR Transfer could fix this :3
i swear i completely forgot about this..but good on OP for being able to solve this on his own..it was like 2/3AM here when i last replied and i wasnt thinking straight..

You guys have forgotten, 9.2 CTR Transfer could fix this :3

Format it to FAT32 (Windows formats it to NTFS by default and can't format >16GB cards to FAT32), iirc https://www.sdcard.org/downloads/formatter_4/ can format to fat32
EDIT: Remember to backup your data before formatting
Yes, only FAT32I know that the 64GB was NTFS and I formatted to exFAT. I guess that doesn't help for the 3DS then. Do the consoles only read FAT32?