"Moments after two of the Falcon 9’s first stage engines shut down, the remaining seven Merlin engines cut off at an altitude of 80 kilometers, or about 50 miles, and a velocity of Mach 10."
If 2 engines were shut down before the rest, it happened only fractions of second earlier. I could not see it happening in the video and cannot find any mentions of it besides your link. Dunno if it even happened since that article is pre-launch flight description.
There is no 2 engine shutdown in the flight plan provided by nasa.
https://www.nasa.gov/sites/default/files/files/SpaceX_NASA_CRS-5_PressKit-105.pdf Approximately 157 seconds into flight, the first-stage engines are shut down, an event known as main-engine cutoff, or MECO. At this point, Falcon 9 is 80 kilometers (50 miles) high, traveling at 10 times the speed of sound. Four seconds
after MECO, the first and second stages will separate. Eight seconds later, the second stage’s single Merlin vacuum engine ignites to begin a seven-minute burn that brings Falcon 9 and Dragon into low-Earth orbit.
But even in your reply you admit that they use less than all 9 engines for entry and landing -- not sure what your particular problem is!
My problem is your claim that "
It's not uncommon to alter the thrust by shutting down one or more engines" is not true in context of doing so during ascent:
If the max thrust of a rocket stage is equal to it's weight then it will accelerate at one g initially (in space outside of a gravity field) BUT, since propellent often equals 90% or more of the entire mass the acceleration at the end of the burn could be 10g's and that's not good with people onboard and it's not wise to design and build a rocket stressed to handle 10g's as the extra mass needed would not be helpful -- so, being able to reduce thrust is important! Operating a rocket engine at partial thrust comes at the penalty of lowered ISP so it's better, where possible, to shutdown one or more engines so you can run the remaining engines closer to rated thrust.
And even during descent, they are not shutting down the engines. They fire part of them. A big difference.
Looks like instant shutdown of all engines. 18:40