The pre-press heroes of InDesign and Acrobat, are the Separations Preview Panel and the Ink Manager. I get files from customers that have more than one Reflex Blue swatch. Most likely, there are or were different people working on the file. Someone used Reflex Blue C, someone else RB U, RB M, RB CVC Reflex Blue, and a user defined, My Reflex Blue. All of these versions of Reflex Blue are a reality. Some apps, when Reflex Blue is defined, names it plain ole “Reflex Blue.” The C designation comes from the coated library, U comes from the uncoated library, M from the matte library, as far as I can tell, CVC means it was set up in an RGB file, because when I see CVC, it has an RGB icon next to it (I have not been able to recreate a CVC swatch at this time). The user can also define a color and name it Reflex Blue, even if it appears Purple on the screen.
The problem with all these swatches is output. They all want to be Reflex Blue separations for the press. Reflex Blue, no matter what designation, all comes out of the same can. The designation determines how the proofing device handles the color. In reality, if all these inks came out of separate cans, the shop would be buying lots more ink, and that would reflect in the print prices. From InDesign, Window > Output > Separations Preview show you all the active inks in the file. From Acrobat, Advance > Print Production > Output Preview. This will help you determine, if you have multiple versions of a color in the file. I have seen files with three versions of the same color in the file, I may have seen four versions once. I use Ink Manager from either InDesign or Acrobat to set up alias names for the duplicates and got one plate. Most of the time I use InDesign. At this time, there is no Ink Manager for Illustrator, though the CS4 version does have separations preview.
I have a link to a pdf file here. You can download and experiment with it. You can check out the print production tools with Acrobat, and/or place the file in an InDesign file to see how the Separations Preview and Ink Manager work. All of these swatches will also look different on the screen, especially the user defined swatches that I dropped in. Once the colors have an ink alias, they will all appear the same on the screen.
I hear a question from the guy in the back with the sunglasses, “Shouldn’t the file be corrected before it goes to press?” Yes, if time allows. And the young lady in the Hawaiian shirt, “Can’t you just delete swatches and replace them with one swatch?” Yes, if the swatches reside within InDesign, you can delete Reflex Blue coated, and replace with Reflex Blue uncoated, but when the swatches reside within placed Illustrator files, they can not be deleted and replaced. If there are two place files, each with a different version of the color swatch, they have to be modified in Illustrator, not InDesign. A color alias can be set for spot to be process, such as Reflex Blue to output as Cyan, process colors can not have an alias set, such as Cyan to Reflex Blue.
If you have inherited a file that someone else has started, multiple color versions are a possibility. Knowing it can happen is half the battle. Having the time and opportunity to correct it, is good, but not always an option. I have set up template files for my customers with the correct color swatches, when the file comes in for print, there are three versions of the swatch. I open Ink Manager and make the file print.