What is a retrofit window permit. I would like to replace my large 3 windows with two smaller windows. It will require adding a few cinder blocks to close in some space.

I have a feeling the window retrofit permit only permits windows
Of the same size in the replacement. Because it states"requirements for replacement of existing windows and door"

I guess I am in for a remolding project and a different type of permit

There are codes as to the amount of "lights" in a room. This means the amount of glass area vs the floor area. I would check with your city as to what the codes are. Making a window smaller is much easier than making it larger (no header work etc). Good Luck!