If a game is using old encryption (which is usually released before Oct 2013), then you can use the following method, if you don't have a Pasta/NTR platform:
For old encryption 3DS game's 3DZ ROM users, or new encryption legit cart users:
1. Get the 3DZ ROM (or legit cart)'s header.
2. Use Sky3DS template editor to replace Sky3DS ROM's template with your header.
3. Open 3DZ sav (or legit cart sav) & Sky3DS sav with hex editor.
4. Replace Sky3DS sav's 0x58-0x80057 (if legit cart sav is 128KB, then 0x58-0x20057) with the whole 3DZ sav (or legit cart sav).
5. Import both modified Sky3DS ROM and Sky3DS sav back to Sky3DS MicroSD.
Done.
For old encryption 3DS game's 3DS ROM users:
1. Use GatewayROMPatcher to import Sky3DS Template's header into 3DS ROM, or just dump Sky3DS with GW Launcher.
2. Copy the modified 3DS ROM (you should have total 2 copies after this) and rename one of them into .3DZ.
3. Rename your 3DS sav into 000400000FF40A00.sav.
4. Mount 3DS ROM and use SaveDataFiler to export save.
5. Mount 3DZ ROM and use SaveDataFiler to import exported save.
6. Open 3DZ sav & Sky3DS sav with hex editor.
7. Replace Sky3DS sav's 0x58-0x80057 with the whole 3DZ sav.
8. Import both modified Sky3DS ROM and Sky3DS sav back to Sky3DS MicroSD.