SaveMiiFrii should work, providing you have a disc with an update above your current one.
I'm not sure what update is installed by metroid prime trilogy, but I guess it's 4.2 in which case you need to wait until there's a game out with the 4.3 update.
Do you happen to have priiloader and bootmii?
In that case you could restore a backup (if you got one) or follow this guide if your bootmii is installed as boot2.
your last option would be to follow this guide to reprogram your NAND