If you have a discrepancy when raising the final invoice for a job created from an estimate, this is the result of the fact that the values of the initial invoice have been edited.
The final invoice will always pull the initial figure from the estimate invoice schedule, not the actual invoice itself.
The reason for this is because the customer has agreed to the terms of that estimate and the invoice schedule
Note: If you tend to edit the initial invoices you can put the value in the 'On completion' field and simply raise a partial invoice after you have accepted the estimate.
You can resolve this scenario with a small system workaround:
Raise a credit note for the initial invoice amount, and any other invoices you have created.
Go into the original estimate and clone it.
Amend the invoice schedule to include the correct values (If you are creating an initial invoice again, ensure it is the correct amount).
Accept and create a new job.
Complete the job as necessary, you can add a note referring to the other job number to reference the diary history there: Job notes and communications.