We actually have a spreadsheet form that prices and summarizes change orders.
You just put in the extra labor, at whatever price was agreed to up front, and the price of the extra parts plus a modest markup (also agreed upon up front).
If parts are deleted, the cost of those parts is a deduct, not including the markup. Costs associated with returning the parts, if any are added in such as shipping and restocking fees.
The labor in the C.O. includes the time it took to create the change order, the time it took the shipping clerk to repackage any returned goods, and whatever other labor is associated with the changes. Engineering, drawing and BOM updates, whatever.
Usually we just print out the summary sheet and ask them to sign on the line where it says approved. The fact that we have a system in place for this kind of thing, and that it is disclosed upfront tends to all but eliminate complaints about change orders.
It's not unheard of, but admittedly rare, for a customer to end up with a net deduct.
Most of the time it is the engineer who prepares these things, and most of us are unwilling to nickel and dime customers so a few hundred dollars on a $50,000 project won't result in a C.O. most of the time. We do keep track of the changes though, so if they start to get burdensome we can send the customer a C.O.