I think R-Wipe & Clean could clean up the Safe Browsing database. The Chrome updates it regularly anyway.
I heard that the contents of this database may depend on the websites viewed in the browser.
Chrome Safe Browsing
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Discussion on the R-Wipe & Clean and R-Crypto software
Discussion on the R-Wipe & Clean and R-Crypto software
Re: Chrome Safe Browsing
Thank you for your suggestion. I've passed this to our developers.