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That worked for me when I had to replace the siphon in my toilet (the diaphragm was ripped so even a manual pull of the metal bit didn't make it flush properly).
Only tricky thing, from memory, was the need to undo a massive plastic nut (60mm or so in diameter I think) to be able to remove the siphon. I ended up cutting a bit of wood into a makeshift spanner as nothing I had would fit something so big.
If you need to empty the cistern, just stop the ball cock from dropping and the valve won't open. Flush the water out, job's a good'un. I don't see why you'd need to stop the supply anywhere else.