I'd unfortunately second @Capeman 's suggestion. Enter the favorites list, and just press Y until they're gone. There's no way to clear it in a single step.
If you scrape those games again though it might clear the favorites flag, depending on the scraper you're using and whether it overwrites existing metadata. That's also an option.
Why exactly are you trying to clear them, though, just out of curiosity? Removing and adding them back won't get you any metadata for those games. You need to scrape them. Probably they weren't scraped as setting then as favorites added them to the gamelists, and the scraper might skip games that already have entries there?