Yes, that's right. If the Council know of the problem, then indemnity is not possible. The reason being that they could (theoretically) claim on the policy.
I still can't understand why you can't just get it signed off now. I've known plenty of cases where this has come to light after many years. Firstly, I would ask Building Control exactly which inspections have been carried out, and which have not.
The fact that the flats were sold initially, and again recently makes a complete mockery of the situation. Bear in mind that this is all most likely coming from the buyer's solicitor alone. I doubt if the buyers care. Solicitors today can be an absolute pain in these cases. They are protecting their own positions regarding "duty of care", and possible litigation.
Solicitors are paid to do what they're told. The buyer can simply instruct them to get on with it. Once everyone is in the picture, the solicitor has done his job. There would be no threat to them; the onus is on the buyers themselves.
Given the previous sales history, it is idiotic to raise any issue now, but, remember that this could all come up again when the buyer eventually sells. You know what the reality is in property ......... the more time passes, the less the threat of successful litigation.
Having said all that, I'd still like to see what inspections are outstanding. Remedying this would still be the most satisfactory way to go.