Sadie,
Bear in mind that, as far as I know, the Council will give an initial decision within 8 weeks of receipt of the planning application, but there is then I think a 5-week appeals period before a final decision is made as to whether or not to grant planning permission. I'd say it is this final decision that you would have to wait on from a legal point of view so that would delay your signing further.
It might also be prudent to consider in advance what your options would be if the Council do not give permission for retention of the work, or if their permission is conditional on certain other works being carried out (e.g. block up a window that overlooks a neighbouring property).