This is a perfectly clean NG+ save file that has all characters at level 1 (zero champion levels), all allies are at "Champion" Friendship (nothing greater than 3 friendship), and can be setup so you have Ultimate 3 difficulty unlocked.

1) Should backup your SaveGames folder here:
%USERPROFILE%\Documents\My Games\Marvel's Midnight Suns\SavedSteam \SaveGames

2) Then turn off Cloud Sync on Steam

3) Delete all files within the SaveGames folder except the save with U3 difficulty unlocked (for some reason the NGPDataSaveSlot.sav does not seem to capture this independently).

4) Copy the file into the SaveGames folder

5) Run the game