Most extra work is originated from inspection reports during a turnaround. Sometimes the extra work originates from other sources (Operations / Production, Engineering, Process, etc.).

The scope of the extra work should be developed, with all necessary steps, including inspection and testing if required. You can then add this work order to the schedule, and report progress against it. Even if the work has been done by the time you learn about it, go ahead and develop the scope and include it into the schedule. Then you can post progress against it, and your reports will reflect the increased manhours for the turnaround and the impact on overall progress and earned value analysis.

Be sure to code the extra work as such, to sort out the costs after the turnaround is over.

The extra work order should also contain a reference to the main work order that covers the equipment being repaired. This will help in scheduling, and later for historical reference.