Check your Unpaid Edits Handling setting - it decides what happens when a customer changes an order but doesn't pay before the window closes.
The two options:
Roll back unpaid changes to the last paid state (recommended) - the order reverts cleanly.
Keep unpaid changes - changes stay; a removed-but-unpaid item can leave a refund owed, and an added-but-unpaid item leaves money owed to you.
What to do: set the handling you want (Order Edits tab), and turn on Allow Item Removal & Refund so refunds for removed items process automatically.