This has something to do with the game saving your files/ your progress on the Fatshark servers. This really could be fixed, i didn’t come around reporting it as i always forgot…
When you open chests and get new items/favour them afterwards and close the game right after, the ‘new item seen’ and the favouring don’t get saved (for some reason). Item creation, re-rolling, and loot in general don’t get reset, no worries.
To circumvent it until it is fixed i figured out you can force the game to safe, and then close the game. You can do this by switching character (game has to remember your last played when opening the next time) or starting a mission (you can close it right after opening the portal).