Hi, I have 20 years of sash window repair so maybe can help. Dare I say, if you can fill it, do so, but hack out rotten, use wood hardner before filling and sand to finish.
Or if you need a new sill, buy a dvd on how to do this job, it is involved. but here is a short. bullet point: strip down sashes, weights and leave only the frame. 2. saw cut accross the pullystyle (inner frame) to just above the weights pockets. 3. cut pins holding in lower pullystyle and remove including the weights access. 4. with both sides now removed, the old sill will now lift (subject to more nails), your new sill can be cut to the same specs as the origional, and all replaced with a run of silicone under it as per building reg.
This is a skilled job.
martin sullivan, January 2011