still it is not clear as if you have stock mismatch you should perform a physical inventory process.Movement type 562 is reversal for Initial stock upload. what steps is he following when you mentioned "So, using MM-562 movement type and related TO, he set to 0 the quantities."
when you do initial stock upload upon succesful posting in Inventory management system internally transfer the stock to 998 no TO is required so when you are doing 562 what process/ steps are you following
Also could you please try to create TO in foreground (hope you are using LT04) and share the screen