One of the things that I know is happening is items that are technically in your inventory but are not in the world or in a storage container.
I made a console command available to everyone to dump all of those items at your town banner if you want to use it.
Type this into the console (Ctrl + C to bring up the console):
dump_inaccessible_items
If the items are disappearing and are also gone from your town overview screen, then that is a separate mystery.
Thanks all
-Yang