Tested and the answer is NO.
My suggestion is don't use Sky3DS to play anything which makes the savedata important, since EEPROM-Yes saves are inconvertible and easy-to-be-corrupted by even official DiskWriter's backup/restoring.
Forgot this method. Thanks for your remind.CARD1 games, yes you can do with powersaves along with appropriate header as well.
Forgot this method. Thanks for your remind.
But this requires the Sky3DS user to know how SaveDataFiler works and to own a console to convert any save into SaveDataFiler format.