Multiple ID1s
This can occur if you’ve used multiple SD cards on a 3DS and then merged the contents of the SD cards together. This is done to prevent conflicting, valid data from being merged together.
To fix this, you will need to determine which folder contains your data. Usually, this will be the larger (or largest) of the folders. Backup and delete the smaller one(s), then create a Nintendo DSiWare folder in the one that remains and move F00D43D5.bin to that location.