Once all claims in a patent application have been allowed, the Examiner can close prosecution of the application on the merits, even though there may be outstanding formal objections which preclude fully closing the prosecution. The Examiner does this by issuing an Ex Parte Quayle Action.
An Ex Parte Quayle Action can be favorable, because it means you are highly likely to obtain a patent. That, of course, depends on whether you accept the scope of the allowed claims. You can attempt to respond to the action with an amendment. This will be a choice driven by your plans for the patent and the claims allowed. If claims were withdrawn, you may choose to try to bring those into the application. Amendments going to the merits of the case are then treated similarly to those made in response to a final rejection, in which the Examiner can either consider the amendments or refuse to enter them.
Frequently, though, an applicant will accept and correct the formal issues raised in the Ex Parte Quayle Action so that the patent application can issue as a patent soon.