Actually I was going to suggest the same when I read it a few days ago, but I couldnt picture the window sill in my head if you know what I mean.
What hammy says will work, cause thinking back I have done it, not pushed into the cracks though, but sort of opened the cracks up wider, and filled, rubbed down, then filled again till its flush with the rest of the sill.
This might sound daft whats coming next, but again it will work and hold it the filler and prevent it from cracking.
Dilute sparingly a little PVA, whack that on the first filled rubbed down crack, when dry, fill again if its still proud, rub down again till flush, then whack again PVA on the crack.
When dry, undercoat and gloss as normal.
When I go into a job, and they have had cracks that have been filled but have opened up again, I use the PVA trick, and I open thier cracks wider, fill like I said above, and PVA each rubbed down layer of filler, what this does is, the PVA seals the filler, gives it like a hard eggshell feel, and gives the crack protection and helps to stop the crack from cracking again.
I have done this many times on inside jobs, and I even did it one time on window frames, and on a bungelow walls, and emuslioned afterwards and its has held, its worth a try.