When you slide the "Marked as Picked up" button (or Encode on POS for dine-in orders), this means that you have finished processing the order on your POS and would like for the order to disappear from your Order Processing page.
If you are not done processing order but have accidentally selected this option you can double check on the items by pressing the three lines on the left side and going to the "Recent Orders" tab. Here you will find the transactions for the current day and the day before.