If we're talking about the extra utilities coloured blocks, the changes it makes are done on a per-chunk basis, and apply to all of the same initial colour blocks.
For example, if you make a blue brick, and make it yellow, it will change ALL blue bricks in that chunk. Red bricks will remain red, yellow (initial coloured) bricks will remain yellow, even if the blue/yellow ones are changed. It's confusing, but awesome when you get your head around it.
