You can manually mark your job as invoiced from the job card by clicking Mark as ready to invoice:

Then clicking Manually mark as invoiced:

When invoicing in Fergus, you'll be asked if you want to mark the job's phase as invoiced when you Approve your invoice:

If you imported your job phases onto the invoice the checkboxes on the left will be automatically ticked. If your job is finished make sure these are ticked as this will update the job's status in Fergus.