If you are using the actual work order cost to adjust your selling price. Yes, you have a problem.
You need to find a way to "Estimate" your Work Order Actual Cost.
Labor transaction should be post as soon as they are completed.
We have the same problem with our vendors, and when the invoice arrive that difference gets posted as a variance, and I believe it is not part of the Unit/Total Cost.
You can always undo finish production, that will be a little bit late, you already invoiced the job.
But at least it will help you have a more accurate Actual Cost for the next time you want to Estimate that job.
have fun,
Kelloggs