To reproduce the problem:
1) Place an order for Item A (status: Pending)
2) In Stock Central, the current stock of Item A was deducted which is normal
2) In Woocommerce -> Order -> open the order and remove Item A, add Item B.
3) In Stock Central, the current stock of Item A was still deducted but Item B wasn't.
Looks ATUM doesn't do anything on order modification, is it normal?