Complete novice having the same problem here trying to fix my daughters 3ds I thought I did it manually myself and although Freeshop now loads there is no longer any games available for download, she isn't impressed any help would be appreciated.
Did you update to 4.1.2 or a older one? If its the new one. You need to move the files from and change the directories of freeshop from 3ds > data > freeshop over to 3ds > freeshopUm I already did manually enter in the title key