As part of the clean up of prosilver for 3.1, colours.css should be removed and all of the duplicate values moved back to their "original" file. Having duplicate values in two files really serves no purpose and only creates confusion amongst users. It's been a continuing question asked in the forum ever since prosilver was committed. The typical scenario consists of the user modifying the value in one of the "original" files and then wondering why nothing actually changes, only to find out after seeking support that the correct location is colours.css.
I have a working patch for this which I'll link to soon.