You mean an affordable house bought under shared ownership? As far as I can remember, the council's equity is increased every year by a set percentage. You would need to increase your mortgage with the council.
If you are talking about the affordable housing scheme then it is possible to buyout the councils clawback. You will have to get a certified evaluation of your property and send it to the council. Let them know you want to remortgage and they will give you a redemption figure which will include your clawback based on the current value of the property. This is the figure you will need to obtain from another lender or by other means in order to effectively buyout the councils share. I have heard that there are some lending institutions that are not overly enthusiastic about this though I am not sure why as theoretically anyhow it seems to be relatively straightforward as these things go!