You will have to reinstall CFW, and no games or saves from the old console will work in the new console. If you have a NAND backup you can try to restore the save files. If you have no backups then you should delete the Nintendo 3DS folder, because it will just take up space but not be useable.
If you do that, if you ever go online to eshop with the new console you cloned to. The eshop will spaz since the NNID is registered to the old 3ds serial number and remove all purchased items as its not the console that owns them.
Because game installs are encrypted per console. You can't insert an SD from one console and have it work in another. If luigis mansion appeared that means it was installed on that console and the files were on that SD card.