If you are referring to Adagio Invoices or Adagio Receivables, these applications only allow entry of a Job number for invoices, and no phase code. This is how it always has been, whether you are interfacing with Adagio JobCost or Accpac Plus Job Cost. But because you have set the revenue level to Phase, then a phase code is required on the batch. What you are describing is exactly the expected behaviour, based on the setup.

If you want to enter your invoices with either Invoices or Receivables, you will be limited to entering only a job, and if you want to track revenue at the phase level, the phase must be entered into the retrieved Job Cost batch.