Folks! I know a fix to the save redirection issue for some of you are having on SaltySD to work. This is an important guide you need to follow step by step.
Step 1: Disable game patching on your Luma3DS Settings, and then press Start to save configuration and reboot.
Step 2: Once the 3DS family system is rebooted, launch either the physical copy of Pokemon Sun or Pokemon Moon. (Or digital download if you have them installed to the SD Card through eShop)
Step 3: Delete the corrupted save file from by pressing Up+X+B simultaneously as soon as the title screen appears.
Step 4: Start a new game and immediately save at the bedroom of your character's house ingame after viewing the very first cutscene of the main story.
Step 5: Press the Home Button and close the software completely by tapping the "Close" button on the touch screen or pressing X.
Step 6: Launch JKSM if you have it installed. If you don't have it, you will have to find it floating on the interwebz for its latest version, so do that beforehand.
Step 7: Once you have JKSM launched, Go to Cartridge, then go to Save Data Options, then choose Export Save. (If you have the digital download copy of either version, you can go to SD/CIA, then pick either of them that way through a list of games and apps stored in the SD Card or Micro SD Card if you are using N3DS/N3DSXL before choosing Save Data Options, and then picking Export Save.)
Step 8: Once you chose Export Save, select "New", type in the word "main". Press A when finished. It will store the new save file on JKSM's own separate folder stored in your SD Card as it is exported successfully. It takes around one second to export the save data. A message will show saying "Complete!", press A to continue. Exit JKSM.
Step 9: Turn off your 3DS completely, then eject the SD Card or Micro SD Card. Insert the SD Card or insert the Micro SD Card into the Adapter and insert that into your computer.
Step 10: On the root of your SD Card, go to the JKSV folder, then go to the Saves folder, then go to Pokemon_Moon or Pokemon_Sun folder, double click the folder that says "main", and you will see your new savefile for the corresponding version you want SaltySD to overwrite.
Step 11: Copy that new savefile and paste it onto this path "sd root (meaning the drive letter of your SD Card automatically set to):\saltysd\SunMoon\". Make sure that the savefile is corresponding to the game's own internal savefile to have it completely matched. Sun's "main" savefile on SD for Sun physical/digital, Moon's "main" savefile on SD for Moon physical/digital. PLEASE DO NOT MISMATCH THE SUN OR MOON "main" SAVEFILE FOR THE WRONG VERSION; doing so will corrupt the save and you'll have to start the whole process over.
Step 12: Eject the SD card/MicroSD card safely and reinsert it to your 3DS.
Step 13: Hold the Select Button before pressing Power. Keep it held for the system to boot into Luma3DS Settings.
Step 14: In the Luma Settings, enable game patching, and then press start to save configuration to reboot.
Step 15: Once your 3DS is rebooted, launch Pokemon Sun or Pokemon Moon.
Step 16: Once you have launched Pokemon Sun or Pokemon Moon with the SaltySD patches applied, load up your internal save file. Try overwriting the "main" save if it already has existed. If it works for the correct version you are on, then you did it successfully as you now have an overwritable "main" save file. If it didn't work, then you must have did something wrong to miss a step. Go back from the start and work your way up to resolve whatever you screw up to get it working.
This is the proper way to make an OVERWRITABLE save file for Pokemon Sun and Pokemon Moon. Hope this mini-guide will be of use to you.
Step 1: Disable game patching on your Luma3DS Settings, and then press Start to save configuration and reboot.
Step 2: Once the 3DS family system is rebooted, launch either the physical copy of Pokemon Sun or Pokemon Moon. (Or digital download if you have them installed to the SD Card through eShop)
Step 3: Delete the corrupted save file from by pressing Up+X+B simultaneously as soon as the title screen appears.
Step 4: Start a new game and immediately save at the bedroom of your character's house ingame after viewing the very first cutscene of the main story.
Step 5: Press the Home Button and close the software completely by tapping the "Close" button on the touch screen or pressing X.
Step 6: Launch JKSM if you have it installed. If you don't have it, you will have to find it floating on the interwebz for its latest version, so do that beforehand.
Step 7: Once you have JKSM launched, Go to Cartridge, then go to Save Data Options, then choose Export Save. (If you have the digital download copy of either version, you can go to SD/CIA, then pick either of them that way through a list of games and apps stored in the SD Card or Micro SD Card if you are using N3DS/N3DSXL before choosing Save Data Options, and then picking Export Save.)
Step 8: Once you chose Export Save, select "New", type in the word "main". Press A when finished. It will store the new save file on JKSM's own separate folder stored in your SD Card as it is exported successfully. It takes around one second to export the save data. A message will show saying "Complete!", press A to continue. Exit JKSM.
Step 9: Turn off your 3DS completely, then eject the SD Card or Micro SD Card. Insert the SD Card or insert the Micro SD Card into the Adapter and insert that into your computer.
Step 10: On the root of your SD Card, go to the JKSV folder, then go to the Saves folder, then go to Pokemon_Moon or Pokemon_Sun folder, double click the folder that says "main", and you will see your new savefile for the corresponding version you want SaltySD to overwrite.
Step 11: Copy that new savefile and paste it onto this path "sd root (meaning the drive letter of your SD Card automatically set to):\saltysd\SunMoon\". Make sure that the savefile is corresponding to the game's own internal savefile to have it completely matched. Sun's "main" savefile on SD for Sun physical/digital, Moon's "main" savefile on SD for Moon physical/digital. PLEASE DO NOT MISMATCH THE SUN OR MOON "main" SAVEFILE FOR THE WRONG VERSION; doing so will corrupt the save and you'll have to start the whole process over.
Step 12: Eject the SD card/MicroSD card safely and reinsert it to your 3DS.
Step 13: Hold the Select Button before pressing Power. Keep it held for the system to boot into Luma3DS Settings.
Step 14: In the Luma Settings, enable game patching, and then press start to save configuration to reboot.
Step 15: Once your 3DS is rebooted, launch Pokemon Sun or Pokemon Moon.
Step 16: Once you have launched Pokemon Sun or Pokemon Moon with the SaltySD patches applied, load up your internal save file. Try overwriting the "main" save if it already has existed. If it works for the correct version you are on, then you did it successfully as you now have an overwritable "main" save file. If it didn't work, then you must have did something wrong to miss a step. Go back from the start and work your way up to resolve whatever you screw up to get it working.
This is the proper way to make an OVERWRITABLE save file for Pokemon Sun and Pokemon Moon. Hope this mini-guide will be of use to you.