Hello Jiri,
There are other dependencies for the cycle limitation other than just the sectors. The flash is divided down from the full bank to blocks then to sectors. For the program flash there are multiple sectors within individual blocks and the cycling will impact all sectors within that block. In other words, if you have 2 16kB sectors within a single block and one of these sectors contains a boot code such that you are operating from that sector while programming the other. The cycles on the sector being programmed will impact the first sector that is only being read.
For the data flash, we specifically design the blocks so that there is only one sector within each block. This approach is less efficient in some ways but allows for the higher cycle count.