Something update from #6's quote of my old response:
If you have a 2nd hacked 3DS, or only one 3DS with either of
- SysNAND 6.0-9.2 + KeyY 6.0 (Post-Oct-2013) game
- SysNAND 4.1-9.2 + KeyY 1.0-2.2 (Pre-Oct-2013) game,
you can use SaveDataFiler + CFW method instead of hex editor injecting .zav to DiskWriter .sav method.
GW side
1) Rename your .sav/.zav into 000400000FF40A00.sav (MT users don't need this step)
2) Mount the game
3) Open SaveDataFiler and export CTR card
4-1) Copy exported "filer" folder to 2nd 3DS's SD/MicroSD root, then boot 2nd 3DS's CFW (for 2nd 3DS)
4-2) Boot CFW (for only one 3DS)
CFW side
1) Insert Sky3DS
2) Open SaveDataFiler
3) Delete CTR card's Secure Value (if your game is Pokemon or other anti-save-restore games)
4) Import exported save to CTR card
I forgot whether Save Dongle dumped save is the same as GW .sav/.zav format or not.
If yes, use it as a GW .sav/.zav and follow all the above steps to convert.
If no, I have no idea.
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For the hex editor injecting .zav method:
1) Change Sky3DS Template with .zav tagged header
2) Export Sky3DS save with DiskWriter
3-1) Replace DiskWriter .sav's 0x58-0x20057/80057 with the entire 128/512KB .zav (for Card1 save injection)
3-2) I FORGOT IT!! (for Card2 save injection)
4) Import the modified DiskWriter .sav