The Met Location does not change when a Pokémon is traded. The only time trading effects the location is if the Pokémon was traded while it was still an egg and that only changes how the egg was obtained. Also You can not make legit Pokémon at best you can make a legal Pokémon. A legit Pokémon is a Pokémon obtained during normal game play and has not been modified by any means with software or hardware that isn’t licensed by Nintendo, Game Freak, or the Pokémon Company.
When Sword and Shield is officially released, PKHeX should get an update, if it all goes well.
Of course it all depends on whether the save encryption is hacked etc. Be patient.
I appreciate that a lot. Crazy how me randomly using the program brought up an issue that others hadn't faced yet or hadn't posted about.
As a temporary solution, I was able to fix every single Pokemon in my save file by manually setting their Displayed and Language flags. So all is well that ends well.
Thanks for reporting, should be fixed in the next release
As the program grows bigger, lazy direct manipulations become harder to maintain. I've reworked things in the past few months to more closely match how they're manipulating data in the games (block objects doing the logic), so small hiccups aren't impossible!