I also have this exact issue, except I have 40,000 Windows 😀 (They were accidentally imported from Safari and now I can't get rid of them, presumably becuase of iCloud syncing)
Would be great to have the ability to just delete all windows with a single button, maybe in advanced settings. (Because with 40,000 of them even selecting all and then deleting in a list like with emails wouldn't be practical)
Alternatively, would it be possible to delete the file/DB on disk that these are stored in?