Problem changing colours to art brushes - Illustrator CS6

Greetings!

For a large branding project I have produced a set of illustrated backgrounds that have been created using bespoke art brushes which I then saved in a Graphics Style swatch. Because we’ve had to change the colours from the original set I thought it cleaner that I expand the artwork and change the colours that way. We need 4 colour variations for each set. The problem has been that this has made the files huge. So big it’s becoming a real issue working with them.

So plan A was to create patterns out of the initial illustrated tile. This helped with file handling but time spent saving is becoming ridiculous.

Plan B was to change the original files with all the effects intact. I’ve managed to colorise in the art brush option box under Hue shift. I’ve highlighted the colours I want in my swatches folder and all seemed to be working splendidly. However I decided to test a press quality pdf from this file and the colours are now different in every CMYK channel. Even spot colours are coming out as process files. I’ve tested this through Indesign too and the same result. I’ve checked that my Creative Suite and Acrobat colour management is all synchronised and it is. So all I can think is that it’s the colorising that is giving me a false colour.

Any help would be most appreciated. We are upgrading to CC in a few weeks so I don’t know if that might help. The problem is I need to resolve this asap really and I’m going grey very fast 😉

Many thanks