I think it is fine to have an A and B final with however many paddlers you want in the A final. But, the best of the 2 runs should count for the B final and the A final could either be the best of 2 runs or the final run only as their first run was still a counting run as it enabled them to qualify for the final).
If there were 50 paddlers with 2000 points max, then the points would be
1st 2000, 2nd 1960, 3rd 1920, 4th 1880, 5th 1840
11th 1600, 12th 1560, 13th 1520, 14th 1480
Only those in the A final can get the top set of points and those in the B final getting the lower set of points e.g.
So, if say 10 qualify for final A, then those in the A final could get 2000-1640 points and those in the B final could get 1600-40 points i.e. the best position for the winner of the B final would be 11th.