hello, I was in this same predicament, basically our shotfall was 30,000 which on our share amounted to 10,000 shortfall. Luckily this happened to 3 other flats before ours so the HA was very very quick and it took them 7 days to authorise the shortfall. To be honest within this climate they will not want to loose a sale. It can however take upto 6 months for the authorisation, I would suggest just being firm at the end of the day you do not want to buy an apartment no matter on what scheme that is not worth the money and let them know you will just go elsewhere. I am sure they will down value on a small figure like that.
I would suggest researching prices around that area and then sending them in to back up your case as now we have got our apartment for 10,000 less than the average around that area.
Good luck and anymore questions on shared ownership dont hesistate to ask as I have just completed and know the stress and complications that come across.