Look at it this way:
Start) 10,000 gallons of water and 12 lbs of CYA
1,000 gallons evaporate
Middle) 9,000 gallons of water and 12 lbs of CYA
1,000 gallons of tap water added
End) 10,000 gallons of water and 12 lbs of CYA
The key point is that when water evaporates the CYA stays in the pool. CYA doesn't evaporate. The water comes and goes, the CYA stays.
You start and end with the same amount of CYA. In the middle, when the pool is low, you have more ppm of CYA than at the start or the end (but usually not enough different for it to be obvious in testing).