You don't need to go through system setup. I think you only need to at least let it boot up so you get to the language select. Then power off and restore data folder and contents of SD card.
Though if you are migrating data from a different model 3DS, you may want to exclude the config system save data (refer to 3DBrew for location). I found that my LCD screens were dimmmer and had noticable scanlines afterwords and that issue was immediately resolved when I removed the config save file. Doing so will make the system act like it was formatted. Don't worry, everything is still there. Just redo the system setup. The only thing I noticed being lost was my Mii. I had to redo my Mii. Mii Plaza however appears to be fine. Just the primary Mii seems to have been effected.