They are most likely used in an image placed within the InDesign document.
Use the links panel to identify .ai and .eps files and open them in Illustrator to locate the Spot Colour.
However, you don't really need to delete them as you can convert the Spot colour to CMYK using the Ink Manager.
In the Swatches Panel go to the sub menu (top right of panel) and go to the Ink Manager
Choose "Convert all Spots to CMYK" and also select "Use LAB values"
They might be in a style someplace which is why they show as used, but that shouldn't prevent deletion, so a more likely explanation is they are left over from an imported object that has since been deleted or modified, and ID just hasn't gotten the message. Export to .inx or .idml may fix that. See Remove minor corruption by exporting
If that doesn't do it, are you sure you really care? If they are not in use they shoudn't generate a plate, so they are pretty benign, but I can understand the urge to clean them out. Can you open the swatch definitions for them and redefine them as process (rather than using the ink manager)? Does that allow for deletion?
If not, the old standby for removal of problems swatches has been to make a new doc and add swatches with exactly the same names, but define them as process in the new doc. Add the new doc and the one with the problem to a ne w Book file, and set the new doc as the source for synchronizination, then synch just the swatches. Delete the book and the new file and you should be able to remove the swatches from the original.
I've seen this is the past with prior versions of ID, and while it may not matter in the end, I'm a fan of having very tidy documents.
I've found a solution to be to:
• Create an image with the same spot color as you want to remove (be sure the name is exactly the same)
• Place that image in the target document
• Delete the image you just placed
• The offending swtch should be 'unstuck' and you should be able to delete
Delete individual swatches
When you delete a swatch that has been applied to an object in the document, InDesign prompts you for a replacement swatch. You can designate an existing or unnamed swatch. If you delete a swatch used as the basis of a tint or mixed ink, you will be prompted to choose a replacement.
- Select one or more swatches.
- Do one of the following:
- Choose Delete Swatch in the Swatches panel menu.
- Click the Delete icon at the bottom of the Swatches panel. Note: You cannot delete spot colors that are used by placed graphics in the document. To delete these colors, you must first delete the graphic. However, in rare cases the spot color cannot be removed even though the graphic has been removed. In such instances, use File > Export to create an InDesign Interchange (INX) file. Then re-open that file in InDesign.
- InDesign asks you how to replace the swatch you’re deleting. Do one of the following, and click OK:
- To replace all instances of the swatch with another swatch, click Defined Swatch, and choose a swatch in the menu.
- To replace all instances of the swatch with an equivalent unnamed color, click Unnamed Swatch.