When you place a PDF file, EPS graphic, or Adobe Illustrator (.AI) file, names of spot colors used in the graphic are added to the Swatches panel in your document, so that you can be aware that they can cause additional printing costs later, and also so that you can use the spot colors in your document.

If the graphic you are importing contains a spot color with the same name as a spot color in your document but different color values, you will be asked whether you want to use the color values in the imported file or the ones in the document.