I know the reason now. I just covered all files to the root of the backup folder...I didn't realize there is a save_data folder in the backup...The system_data and mii, spirits folder are just exactly the same as the root of backup folder...
I backed up the original save file and use all unlock file to cover it then I restored the save folder. It just doesn't work.
The game rom I downloaded was .NSP file. Could this be a reasom?
I used Checkpoint to restore this save file but the characters and spirits doesn't unlock. It just as same as the beginning without any progress. BTW, I am using SX OS too.