The cleanest way to cut fiber cement siding is by using siding shears.
Cutting cement board siding.
These are specialized to reduce the dust caused from cutting these planks.
One way to eliminate cutting or at least keep it to a minimum would be to remove the entire piece above the window flash the window and then replace the siding.
For a slow but virtually dustless way to cut siding use power.
To keep dust to a minimum use a circular saw that s equipped with either a dust collection bag or electric fan that.
Typically siding shears use air pressure to power them and they shear or cut the siding like a pair of scissors.
Use a specialized blade used with the saw such as mikita hardiblade or dewalts filber cement blade.
If any cutting needs to be done to allow for the added flashing than it can be done on the workbench with a pair of siding shears zero dust.
You have to make the cuts very slowly.
The advantage of using the circular saw is that you can cut more than one board at a time.