Hmm odd. Okay, let's see if I'm missing any steps:
1) Edit save in PkHex, then Export SAV > Export Main
2) Created a new folder for the save file in root > JKSV > Pokemon Shield > Save File 3 in the SD Card
3) Saved file (main) in that folder. (The "main" file doesn't have a file extension). There are no other files in that folder besides the "main"
4) Insert SD Card into switch, boot Switch CFW, open JKSV (not in applet-mode)
5) Select Pokemon Shield, navigate to "Save File 3" folder
6) Select "Restore"
Am I missing something in my process? Should I try another way to restore the save file? Doing this with Pokemon Sword works every time, so I'm not sure what is going on here.