Just a random thought: use the SD card decryptor from Decrypt9 or rxTools, generate xorpads for that file for 1 nand, and do the same for the other, decrypt the old NAND's save, replace the save from the new NAND with that of the old NAND, re-encrypt the old NAND's save with the new NAND's save xorpad, done.
I don't think that will work though, unless the magic anti save-restoring value is stored in that .sav file.
It's possible, just a bit difficult and very time-consuming with the current tools available.
For the method I will explain, you will need to downgrade to 4.5, and upgrade when the process is done, as you don't seem to have any other way of running SDF available. I warn you that I haven't personally tried to do this, but in theory, this should work.
I'm assuming you have 2 SD cards, one with the old NAND, and one with the new NAND. This can also be done with just one SD, but that's even MORE time consuming.
You will need to have a save file created on your new NAND, and verify you can play the game with that save file.
You will need 4 NANDs: Your old NAND, another 4.5 NAND linked to this old NAND, your new NAND, and a 4.5 NAND linked to your new NAND.
You can create the linked NANDs with a copy of your sysNAND, as done by the GW launcher, and link it by moving the movable.sed from the updated NAND to the 4.5 NAND. Warning: this will cause all data from the 4.5 NAND to be lost.
Please note that the linked NANDs need the same SD card inserted as their updated counterparts, to be able to extract their respective save files. The only way to achieve this is by creating a dual emuNAND, or putting the linked nand on sysNAND.
You can use sysNAND to avoid creating 2 new dual emuNANDs. Just be careful and validate that the movable.sed you're transferring is the right size. This can potentially brick your sysNAND, but if you're careful, it has no reason to. Also, remember that all the data on the sysNAND will be lost, unless backed up (which you will do anyway when downgrading).
If both the old and the new emuNAND are linked to the same sysNAND, you don't need to do anything with the movable.sed, and you can just use PBT-CFW and swap SD cards or the "Nintendo 3DS" folder only.
So, once you know how you will manage your NANDs, insert the old NAND's SD card into the console, boot into the NAND which is linked to your old NAND with either Dual emuNAND CFW or PBT-CFW, depending on your setup, with the L button pressed, install SDF with ctrclient instead of devmenu, launch SDF, and back up your save (id can be searched on 3ds.essh.co).
If you're using your sysNAND, and it's unlinked from the new NAND, it's time to inject the new NAND's movable.sed.
Now, do the same process with the other SD card, and dump your save.
Now, this is the important part. We need to copy over the magical unicorn of save restoration restriction bytes, so that the bytes of the old save match the bytes on the new NAND, so it doesn't think it's an old save.
Whip out ure favrit HEX editor, and open the system_data.bin from new save file. Write down on a piece of paper or whatever you have,
bytes 0x12 to 0x16.
Now, open the system_data.bin from the old save file (make backups!), and replace those bytes by the bytes of the new save file.
Copy the old save file to the new SD card, launch the linked NAND to run SDF, and inject the save. Launch the updated emuNAND with rxTools to test it, and you should be all set!
