There is no 'select by colours' that could highlight a quick way to answer your question. There is "Find this color" (just a shortcut for "Find/Change", Color tab, Find Color=the swatch, Search="Document", Type="All Frames"), which normally does the trick for me. Then check one layer at a time (select > all and check the layer list if that little square appears after a layer's name indicating something is selected. Check pages and Master pages (called Parent now). Maybe a style (Character, Paragraph, object, cell, table...) or just something small on the pasteboard is using it. "Find this color" will find uses of a swatch in any layer and any page, including parent pages and the pasteboard. Not sure about hidden objects, but I had already checked for those. That's why I assumed it was a style. Failing all that. I would set the colour to be a spot colour to check the colour separation in InDesign... "Failing all that"? You would have done all that other stuff first? It turns out this was the best clue in your reply - by far the fastest way to solve the mystery. I had to google to figure out where to find color separations, but it's Separations Preview in the Output panel. So I changed that swatch to Spot Color, turned off CMYK in Separations Preview, and scrolled through the pages. The only thing still visible was a small logo inside a PDF of an ad. But that was weird, because placing a PDF doesn't create swatches. (And the logo was black, not the olive green of the stubborn swatch.) When I tried to remove the swatch and replace with black, InDesign crashed. So I realized it was some sort of anomaly. When I reopened, I deleted the PDF, removed the swatch, and placed the PDF again. No more problems. As for your side comment: I used to use a template, but often there are little tweaks I make to improve my styles, and it's hard to remember what I've changed and make the same changes a second time in the template. So it ended up much easier to just consider the previous issue my template. The routine to prep it for the next time only takes me a few minutes.
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