The easiest way to test for these colours is to make them spot colours then use the Separation Preview panel to show each colour only. Anything you see must be using that colour. If all pages are blank for each colour, then you’re clear. If you’re still not convinces you can print separations to either you printer or a PostScript file which you can then distill in Acrobat Distiller then scan the PDF.
Some places where the swatches might still be used are paragraph, character, or object styles. You may have changed the colour directly on a styles object or styled text rather than updating the style. Perhaps you did properly redefine all your used styles but missed some unused styles.
One trick to remove stubborn swatches is to export an IDML then open that file. The swatches will still be there, but you might be able to delete them without the trouble.
Or just go ahead and delete them and repalace with Black. Isn't that what you were trying to do in the first place? ID migh be confused, or there really might be some hidden object on a pasteboard someplace or it might be a style (but you don't have any) or just one of those things. If there's no hidden useage, no harm done. If there is, you want it black anyway, right?
Thanks, Scott ... for reading my whole question, AND for the answer.