Sounds like a good reason to turn off auto-updating. At least you can launch without updating and save everything safely, just in case the Traveller's Chest contents is lost. Alternatively, and a real pain. is to regularly transfer stuff from the Traveller's Chest to another chest or bag that won't/shouldn't disappear. As I mentioned in my initial post, I use Bags Bags Bags which gives me much more reasonable inventory management.
