OK instead of just deleting the image files I set the "show recommendations" option in Calibre's KoboTouch driver and deleted all the old recommendations. Easy. This got rid of most of the extra covers, though there are still a few hundred left.
I noticed one big improvement after deleting over 1000 recommendations from the database: Sync time has dropped dramatically. The "loading content" phase of sync was taking over two minutes before, now it takes just a few seconds.
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