I finally found an easy solution posted at InDesign Secrets Blog... Here it is:
Elizabeth Lass
November 28th, 2007 • 3:53 am • Link
Hi, This actually happens to me quite a bit. I found a good trick online quite a while ago, and I’d like to give them credit, but I’m afraid I can’t locate the source. But the trick goes like this:
When a spot cannot be deleted from the swatches palette, and you know for sure it’s not in use by any artwork, create a rectangle and fill it with the offending swatch. Cut the object and paste it into a new doc with no other swatches. Save it as a PDF set to “Press” or “Print” (don’t let the color be converted). Place that PDF into your original doc, then delete it. In my experience, the bad swatch will now be ‘unlocked’ and you can trash it in the palette. IMO, this is faster than saving over to INX, and shouldn’t cause any further problems. {Thanks for the awesome blog and podcast, btw!!}
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It really works.
