The location of the saves is not depending on your CFW but only whether it's sysNAND or emuNAND.
If you use SX OS on sysNAND, you can just boot into Atmosphère and they are still there.
If you are switching from sysNAND to emuNAND (or vice versa) you should batch backup all saves and then restore them. I don't know how this works with JKSV tbh but it's pretty easy with Checkpoint.
Edit: If a save file of yours is not appearing in Checkpoint, try this:
1. Start that game (so it creates a save it not already done)
2. Start Checkpoint and make a backup
3. Look up your SD card and go into sd:/switch/checkpoint/
4. There you find the saves folder and within a subfolder for each backed up game that has the title ID and the game name in it
5. Find yours that you just created with Checkpoint and replace the save file inside with the one that you want to use
6. Start Checkpoint again and restore that save