Just found the following article that could work with Flux to generate colorful prints once the Software Team provide us mid-stream manual filament change option with layer indication in the Monitor window.
I’ll play the devil’s advocate, I also found this article! Mazuir Ross • Terrible Idea: Coloring Filament with Sharpies
However, I still think it is an interesting idea to try out sometime, maybe with an older, simpler Arduino based printer…
Oh man, you had me thinking of a dropping some ink into my filament oiler. Then I read the second article. 
. Thanks for sharing!
I mentioned the 2nd article, but I am not convinced the nozzle clogging is caused by the ink since the colored ink prints well. Some purging is probably required after color printing to clear the paint remnants from the nozzle. More internet digging is required probably to clear the issues.
Also, I think inking is something to try first with a cheap 3D printer with a easily replaceable printing head.
It’s still unknown until we test it.
Check this video, another idea on how to color the filament. http://www.thingiverse.com/thing:12289
If you know how long filament the print will use, you could apply that technique. Cura gives the length as you slice the item, I don’t use S3D maybe it also gives the length required. If you could find that info and you could apply different colors to layers. For instance 1st 20 layers blue (you have to estimate or find out the length it will be), next 30 layers green etc…
