With the approved CYA test, any number over 100 is in question and should not be trusted. But let me do some math to help you. Lets say that your pool was 9000 gallons, and your CYA was 200. If you drained 2/3, down to 3000 gallons, those 3000 gallons would still have a CYA of 200. But if you add 600 gallons back to fill your pool, now the filled pool would be down to 67.
Do with a 2/3 drain, using the drain and then refill technique (and this is important to differentiate), the best you can do is to take your CYA down to 1/3 of its original value. And due to test accuracy, lets just say that you thought it was 200. It might have been 400 in reality.
So the fact that you are around 100 still seems fair, even if depressing.
When you say exchange, were you simultaneously draining and filling, simultaneously draining and filling with a tarp separating the new and old waters, or did you drain down, and then fill. I ask, because there is a huge difference in outcome.
The problem with simultaneously draining out water while adding in new water without a tarp separation, is that you are not only draining old water with high CYA, you are draining out new water as well. There are too many factors for me to do the math, but as a quick guess, simultaneous non-tarp actions would take my math example above, and rather than getting rid of 2/3 of your CYA, you might only get rid of 1/2 or 1/3, so your CYA might only go down from 200 to 100 or 133.
If you are going to use rain to exchange water, the best way to do this is like this. If you think that you will get 2" of rain in a week, drain your pool down 2" before any rain comes down. Then let the rain fill it back up. This provides the biggest bang for your buck so to speak.