A single entry has to place 3-10, not 12, to qualify two spots; a single entry placing 1-2 earns three. (You may be thinking of GP, where the 11th and 12th place skaters at Worlds are guaranteed two spots for GP.)
The spots are earned by country. If the country doesn't have enough skaters with the minimum score for Worlds, they send fewer than they earned.
For the Olympics, in the past, if a country didn't the amount that they'd earned, then the next country (without any spots) from the qualifying competition was offered the spot. For example, when Gedevanishvili earned two spots, but Georgia didn't have a second Lady, the spot was offered to the next Lady at the qualifying competition (skipping any skater from a country that already owned a spot through Worlds or the qualifying competition). Sometimes countries give up spots because their local Olympic committees have stricter criteria than the ISU.
If the ISU sets minimums rather than using the current system to limit the field to Olympic sizes, then they'll have to determine the deadlines by which the skaters have to make the minimums, or they risk having fewer entries than spots. This is undocumented at this time.