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If the swatch is part of an image, most likely a spot colour, like an illustrator or photoshop file, you won't be able to delete it from InDesign.
You will need to find the image and open it in the appropriate programme and convert that colour to cmyk.
OR in InDesign you can go to the Swatches Panel sub menu (top right) and go to ink manager and select "convert all spots to cmyk" - if your document isn't supposed to have spot colours.
And if none of this works, and you have a file that's slightly broken, which does happen, http://indesignsecrets.com/color-swatches-that-wont-delete.php
You can also set the swatch itself to process, which produces a better conversion than Ink Manager when the color is being spec'd as a tint. You still won't be able delete the color, but it will export or print as a process color.