Hi Jayed ,
Thank you very much for your post.
I am very sorry if Im misunderstanding here, but the WC system handles orders and returns effectively. If you cancel an order the stock is returned so what is in WC should be in your warehouse too.
If you just want to check the physical amount, print the stock report and compare the two off line, or is this not an option? If you find a difference use the stock logs to add or reduce the amount.
Hope this helps.