No. As I said in my earlier post:5. I plug that save data into the encryption machine and it spits out my new save data (this is so my O3DS savedata can become encrypted to the N3DS NAND? Layman here but I think that's the gist)
Generally, the most straightforward way to do this is to install your game from the eShop, start a new save file, export the save data with Checkpoint, overwrite the exported save data with the old decrypted-and-extracted data, and then import it with Checkpoint again. (Checkpoint takes care of all the encryption.)If you just want to preserve your save data, then you can always decrypt and extract that manually on a PC, and then restore it on your N3DSXL using Checkpoint (or JKSM if you don't want to hack your N3DSXL).
(There is at least one alternative method that does not use ninfs and 3ds-save-tool, but that ends with using Checkpoint again anyway, so there's not much point to it.)
If you are sick to death of CFW at this point and never want to have anything to do with it ever again, then you can use JKSM without having to make persistent changes to your N3DS. But people will be much more likely to tell you that CFW is perfect and glorious and that you should have no hesitation about installing it again.