When you do not need to ship your orders automatically, you may set it off and do it manually on the order 

Once yoo have opened the order touch the truck

Touch Ship then the product will have the inventory and available as they should be 

Now from Database > Sales / Invoices > Unshipped

will show the orders that has not been shipped

IF you have too many orders to ship you should go to the web version web.selbuk.com to ship them at 

Settings > Restore > Ship all orders

next click on continue to ship all orders that has not been done yet