You have two options when you raise an invoice:
As a rule you should always use the Progress Invoice option unless the job has been completed and only then should you use the 'New Invoice' button.
The 'New Invoice' option is a final invoice. Raising a final invoice has a significant impact on the job. Any items that are not ticked to be invoiced on the final invoice will be written off.
As an example if you have a job that includes several actual cost items, upon raising your initial 'New Invoice' or final invoice, you decide to untick some of these line items so as to not invoice them this time around, the line items you deselect will be written off, and you will be unable to invoice them in the future. The only way to retrieve these tasks or costs to invoice would be to cancel or delete the invoice.
Raising a New invoice (Final invoice) will remove the job from the invoice list (estimated billings tab on the Invoice Manager menu). Adding a cost or more time will put the job back in the list but the previously written off time will not be available to invoice.
If you have created a Progress invoice rather than a New (Final) invoice at the end of the job and the job is now finished, you can write off the remaining time simply by removing the job from the invoice list from the Financial tab of the job.