Multiple Titles for 1 property

Good afternoon
I have recently purchased a property from the local council, who have taken possession via the court due to it having been abandoned for many years.  I managed to secure planning permission and have now converted it into 2 properties, using an existing extension which was built on the property some 30 odd years ago.  It has now come to light when selling the property, that part of the extension (2nd house) is sat on land which has a separate title which wasn't transferred to me when i purchased the house.  I have attempted to contact the council and their solicitor about this, but am having no luck in obtaining a reply, I would just like some advice on what can be done and where i stand as i believe i will struggle to sell this property.

Good Afternoon Katherine - if you are not the registered owner of part of the land/property then you will struggle to sell it as you state
The only option currently available to you is to press the council, assuming they remain the registered owner, to transfer the legal ownership to you. The alternative is to wait 12 years to claim ownership 
Do speak to your legal rep and escalate the issue with the council as appropriate

The council obtained permission via the court to sell the property and recoup their costs incurred.  The titles always remained in the original owners name as he has and still is uncontactable.  Each title references the other so i am unsure why this hasn't been picked up, but my most pressing problem is having a property on another title and the legal implications to this, i don't seem to be able to get an answer from anyone

Katherine - it all starts with how the title is registered. If there was a court order that enabled the transfer to take place, but the second title was not included, then you need a second transfer to be completed and executed as appropriate.
One assumes that the order identified who was to do what and provided the council (?) with the legal authority to transfer the property to you. If so then they now need to repeat the transfer process for the second title number.
Any 'error' in not including the second title would be down to the council and the conveyancers involved at the time of that first transfer I suspect. It wouldn't be down to HMLR as we presumably updated the registered information as per the transfer/application submitted. We would not have queried the fact that a second title was not included
The key point is that you need a second Transfer to update the legal ownership now. Why it happened and who was at fault can be important with regards who is responsible for getting it done now/costs etc but the key point is the need for that second transfer it seems
 

Thank you for your assistance, that has been really helpful