Before the release of the Colony update, I started The Foundry on Legendary, on Xbox One, then saved and quit (not auto save, but an actual save slot). Days later, I downloaded the Colony update. I then finished The Foundry and started the next Mission (The Halo). I then saved the game (overwriting my previous Foundry save), then quit to play some Blitz.
I noticed it said I hadn’t downloaded Leader Colony yet, so i started that download while I played one game of Blitz, then quit and closed the game.
Next day I booted up the game, built a couple decks (Kinsano & Colony), and resumed The Halo. On load screen, it said the difficulty was Normal. I quit the game, and double checked my stats on the previous mission select screen. The Foundry was indeed completed on Legendary. I’m still on my first playthrough, so I was definitely looking at the most recent mission completion.
Before starting The Halo, I didn’t select a new mission. The game was a continuation from The Foundry on Legendary. The difficulty remained the same in the past for continuations. So, either it’s a bug or the game changed difficulty upon new mission continuation.
EDIT: The game save still says Legendary, so it may have just been an error on the load screen.