Hi Adam,
If I was you I would wait until you get the valuation from the council and see if you are happy with it.
In my case the market value of the property had fallen signifigantly in the time between me paying the booking deposit in August and getting the valuation letter the week before last - the Affordable Homes Partnership had got the apartment re-valued in the meantime and renegotiated the price with the builder. So yes, your clawback may be lowered.
If you are buying under the Affordable Housing initiative and not the scheme (which I think you are), those properties are aquired in a different way than those on the scheme. The ones on the scheme may have been bought by the council in bulk for a certain price at a certain point in time so there is less room for manoevre on the clawback with these, even if the market value does fall before they are actually sold. This might be the case with some of the other properties that people are talking about getting independently valued.
This doesn't seem to be the case with those properties acquired under the initiative. I'm not sure of the exact ins and outs, its v. confusing, but either way, the council/Affordable Homes Partnership will want to be getting the best possible deal for themselves which is good news for you too.
Hope that makes sense & hope it works out for you!