It's not entirely clear what steps you are using to see the issue you mention. Maybe you can write them down so that I can try to replicate. If the issue is replicable, then definitely report it to Adobe using Illustrator Feature Request/Bug Report Form I tried two things to see if I could replicate what you are seeing based on the screenshot you included. Test 1 - Editing an existing swatch that was named with a PANTONE colour name, then turning it to a Book Color. Test 2 - Adding a PANTONE book colour and then merging duplicate colours. Test 1 Created a New Swatch, named it PANTONE 171 C, and defined the colour using incorrect CMYK values, and applied it to an object. I then ensured the rectangle was no longer selected, and selected the swatch in the Swatches panel, and from the panel menu selected Swatch Options. In the Swatch Options dialog, choose Book Color from the As soon as you click OK, the artwork that previously had the green colour applied to it will be recovered using the Book Color. It will do so regardless of whether in the original colour definition you defined the colour as Spot or Process. Test 2 Created a New Swatch, named it PANTONE 171 C, and defined the colour using incorrect CMYK values, and applied it to an object. Then add PANTONE 171 C from the Book Color Library, by clicking on the swatch in the swatch library, in the Swatch Conflict dialog box select Add swatches. Click OK. This will add a second PANTONE 171 C to the Swatches panel. Move this swatch above the green version in the Swatches panel. Then select both PANTONE swatches, and select Merge Swatches from the panel menu. The result will be that the previously green coloured object becomes red. You'd have to rename the PANTONE 171 C 2 swatch to PANTONE 171 C after that.
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