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Finding something that bonds to the stone is likely the trickiest part.
Cement will bond, but if any water gets between (which will invariably happen, no matter how careful you are), the sill will degrade far quicker than without.
The lime mortar companies are usually good to talk to - they've lots of experience, and happy to talk. Try the chap at Mike Wye, or Conserv themselves.
Thanks. It looks kinda simple really, they're not too bad, just pitted and a bit crumbly on the surface so I figured I could just fill with a product and smooth over with a trowel to make it decent but far from perfect. Once painted it'll probably look a lot better.