Only save with crypto version 1.0 will be compatible. If you have 3ds with firmware 9.2 or below, you don't need the dongle, just use gateway launcher to backup/restore save data
Don't spread wrong information. I have tested that GW launcher can't dump Sky3DS save.
Details:
Dumping Sky3DS ROM - OK but ultra slow
Dumping Sky3DS save - 3DS freezes (no response during at least 1 hour)
Restoring Sky3DS save - Write save chip error
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For Sky3DS save importing, please use official or 3rd-party DiskWriter to export the save, and then inject converted .ZAV save with binary editors.
The .ZAV save must match for a .3DZ ROM with Sky3DS Template's header.
If you want to use a .ZAV save with custom ROM header, you should edit Sky3DS Template with official or 3rd-party Template Editor.
If you don't have .ZAV save, you should convert your .SAV save into it.
To convert a header-less .SAV save into a header-required .ZAV save, you should have both a GW-usable console and a GW/MT. Otherwise you can't do any conversion.