I'm pretty sure the ISU throws out the old results at the start of the season rather than on an ongoing basis. At the start of the current season the rankings only included results from 2008-9 (worth 70%) and 2009-10, with no events left from 2007-8. Competition results from 2010-11 simply add points to that, so a top 3 finish should leave Takahiko in good shape.
The following is partly based on guess work and working backwards with the math, because the ISU communication on how rankings are calculated are as clear as mud (pdf link of unhelpful doc
here):
No, it isn't that the result is thrown out, it is that only 2 of the highest points in that category of competitions (worlds, Olympics, 4cc / Euros form their own group apparently) from the current season + the past 2 are counted. Before 4cc, Kozuka had no 2010-2011 poins eligible for that category since neither 4cc or Worlds took place yet this season. So what counted in that group is his 8th place finish at the Olympics last year (worth 574 points), and his 6th place finish at worlds the year before (709 points x 70% = 496). 496 + 574 + various results from the grand prix gave him a ranking point total of 2982. If Kozuka finished 5th or higher at 4cc this season, he'd get a score in that score category higher than 496, which obsoletes the 496 score he got from his 2009 worlds finish. Let's say Kozuka had won gold at 4cc instead, what would his ranking point total be? 2982 + 840 (the points you get for winning 4cc or Euros) - 496 (obsoleted) = 3326. This would put him ahead of Daisuke Takahashi's 3318 ranking points.
But wait, what if Daisuke also went to 4cc? Even if he came in last place, 20th, he'd still get 113 points, which would = 3431 and put him ahead of Kozuka. But why doesn't Daisuke get any points obsoleted in that score category? Because he skipped 2008-2009 completely, he has no score from that season at all in this group and nothing to obsolete. So all Daisuke had to do is show up at 4cc and he'd maintain his ranking advantage of Kozuka.
Phew, did that make sense? No? OK, let me try explaining it without the math.
Basically, Daisuke is somewhat undervalued in the ranking because he missed 08-09. As soon as any halfway decent 4cc results came in he'd get a huge boost in the rankings. Oda has it way over Kozuka because he did far better in placement on the GP circuit both this season and last. Kozuka could not make up for it with just a competition.