Yes I know, but if you want to avoid the cloudiness, then don't listen to the instructions. 😄
There is no right way or wrong way to switch substrate. Just do it the most efficient way you can manage.
For some, it's catching everything and draining the tank. For others, it's scooping out the old gravel as much as possible and replacing it with new gravel slowly without crushing/burying the little shrimps.
I usually catch the shrimp, drain the tank, and replace the substrate. Either way be prepared for a long process.