Not that hard to estimate. Lucara mines ~90k carats per quarter (http://www.lucaradiamond.com/i/pdf/CP-Q12016.pdf), or 360k carats per year. They recovered the OP stone in question after 5 months, and it was not that unprecedented as a sale by them of the Constellation 813-carat stone is also mentioned. So 1 every 6 months or 2 per year is entirely possible at this point. But we'll go with 1 1k stone per year, or 1 per every 360k carats mined. Global diamond output is somewhere on the order of 137 million carats per year (http://www.mining.com/web/despite-de-beers-and-rios-efforts-...). If all mining has a similar rate but they are crushing the big ones, then that suggests that 137000 / 360 = 380 stones are being destroyed each year currently.

Production has risen steeply over history (http://www.gia.edu/cs/Satellite?blobcol=gfile&blobheader=app...) but "The total global production from antiquity to 2005 is estimated to be 4.5 billion carats". So for an all-time estimate, 11*360 + 4500000 / 360 = 16460.

This seems improbably high: surely at least some of those 16k giant stones would've survived? So maybe Lucera's current mine got lucky, or it's unique in providing lots of giant stones. ("It has an enviable share of the world’s heavyweight diamonds. Of the 52 biggest diamonds discovered in the past three centuries, 10 have come from Lucara in the past three years. With modifications under way at the mill, Lucara will soon be able to recover diamonds up to 3,000 carats, and next year, up to 5,000 carats—as big as a softball.") Still, I would personally stay the hell away from giant diamonds as any kind of investment or prestige trophy.