I'm sure many people have experienced this, I am proficient in Illustrator, but this has been one of a few enigmas. Every once and a while in a file, I have noticed that after deleting a color that is definitely not in use(ie there are no strokes, fills, stray paths etc) using these colors. I have made sure of it. I will delete the color from the swatches and as a final pass I like to add used colors and sure enough that color will come back. I tried making sure it's not checked global, didn't work, some I don't even think are global colors, and in fact they are generally CMYK. I often notice that Black and C:0 M:0 Y:0 K:100 don't like to delete from the swatches among some other colors when you delete unused swatches. I thought perhaps they were in guides or something but it's truly unexplainable, and generally with a fresh file if all colors are deleted it'll still leave black white and gray.
Is there any way to fix this? Or ways to troubleshoot better other than creating a debug file and deleting lines of code as recommended in the older forums?