Hello! Apologies for awakening an old thread but I ran into this same exact issue with Scarlet and since this was the only place I could find that got me close to the answer, I thought I'd add some more info to help folks out.
I solved it (without undoing the lock on my mon) by going to each Pokémon you want unlocked, and right click on them, then press View. Once their info is on the left pane, hold down CTRL+ALT and right click on the mon again. Click Legality and on the result screen that says they're good, click "copy to clipboard".
Then, choose a new empty box slot and hold down CTRL+ALT while right clicking on the empty spot, then click Set. You will now have an unlocked, exact replica of your mon.
Once done, export the main save file, put it on your switch, and Restore using JKSV.
Hopefully this helps others like us.
Enjoy your newly freed Pokémon!
