Have a read of your PCN.
Somewhere in it, it will say that representations against the PCN will be considered, but if, notwithstanding those representations, the council serve a Notice to Owner anyway, the recipient must respond in the time and manner indicated on the NtO. Normally, in responding to a formal reps against the NtO, the council will re-offer the discount. But you have yet to submit formal reps.
Whatever you do, DO NOT ignore the NTO or you'll lose game, set, and match.
Councils issuing NtOs before they have responded to informal reps is commonplace, I'm afraid. The legislation is as it is, so we must live with it.