If you use Pio with "Partly shipments" disabled, the orders with missing stock items will still be synced to Pio, but not added to picking queue.
Go to Dashboard > Orders and choose 'Filter':
Choose Stock - Insufficient stock:
The filtered list will show all orders where one or more items are sold out.
Manually add available products to picking queue
If you want to manually add available products in a specific order into a picking queue, click 'Queue items in stock' button:
See more details on how to toggle 'Partial shipments' on/off here: Partially fulfilled orders