We're getting our wires crossed IMO.
Was the keeper entitled as a matter of law to submit reps under reg. 5 (Part 2) late? Yes.
Were they entitled to 'make false reps? No.
Were the authority entitled to disregard? Yes.
Did they? No, they said they didn't receive.
IMO, while the OP doesn't have 'clean hands', this in itself does not relieve the authority of its duty nor remove the keeper's rights.
But when all is exposed, it is highly unlikely that the council would take action.
OP, what proof do you have that you submitted reps against the NTO? You cannot have proof of posting dated 17th, can you, so what proof do you have?
IMO, no proof means the adjudicator* would be entitled to decide not to register the authority's referral as an appeal, which would leave you owing the surcharged penalty.
*- the authority would, if notified by TEC that the OfR had been revoked, be required to refer the matter to the adjudicator who may issue directions. These are normally: show us your proof.