When adding the second player in couch co-op, it will not pull up the second player’s account, even if they’re already signed in. So rather than it being Username1 and Username2, it pulls up the players as Username1 and Username1(2). Player 2 starts out fresh, without any items or progress and without signing into the second Microsoft account, causing any second Microsoft account to lose the items they have in their inventory because they are not signed in under a second account, but as a guest of the first account.
This issue is being tracked at MCPE-222048.