Limequill

If you also check your in-game caught shinies majority of them have a value of XOR = 1. I'm not sure if that's related or not but I just found it interesting cause I have 4 boxes of shinies I caught in-game and all of them have a XOR value of 1 and I have 4 shinies which I have received from shiny give aways on reddit and they have differing values like 5 or 8 etc. Might be related or not but I just thought I'd point it out.

Then change it back to 999 battles or just 1 before the completion and it should work

It worked fine for me when I used JKSV literally 20 mins ago, I changed my held to max and some of the Vitamins, Stat Feathers, Bottle Caps and EXP Candies to 999. I do this as to try not overly changed to much in PKHex and just do it within the confines of the game. Used JKSV and it reloaded fine and is working for me

So you mean to say that encounters follow the same seed table as the Raid Dens in SwSH and S/V? Then would generating from the encounter table also be flagged?