Paul - all understood and appreciated but it appears that you have all the registered information and a resolution re the issues raised by the council is very much one only you/they can now resolve. In light of their threat of legal action I would recommend seeking legal advice as appropriate
We register the general boundaries and not the exact legal boundary. Establishing the precise position of the legal boundary is often a matter only neighbouring landowners can decide between them.
Our
PG 40 supplements 3,4 and 5 explain this in more detail but it's very much legal advice you need here