Well, I have multiple backups of com.sweetpproductions.SafariCookies.plist going back several years.
I tried copying over the most recent, as well as several from across different months this year, and one year+ ago...NONE of them restored the favorite cookies!
I think that I figured how Cookie and SC work-- that what happens is that they overwrite Safari's own Cookie list. So, the key here is NOT the .plist for SC or Cookie, but Safari's own Cookies.plist that had been deleted.
I'll try an older one, from last week, and see.
SUCCESS!
It seems to me that you absolutely need to have Cookie, on its first run, make a backup of Safari's Cookies somewhere and alert the user that it's available for a restore if needed. In fact, Cookie should have a button for "Restore Previous Favorites List" to cover all disasters. There always needs to be a fail-safe, backup. But just as central is for Cookie to automatically bring over the previously-- years worth--saved set of favorite cookies. Without that, the program creates all the frustration and hassles I've gone through-- and I'm a backer, supporter, and believer in Safari Cookies.
I also agree with several reviewers on the App Store who said that the interface and the language in the interface needs improving. The phrase "Configuring Unwanted Data" gets into double negative terrain linguistically when trying to decide whether to check or not check.
In any case, now that I've figured this out, I may even try Cookie again-- yes, I'm a glutton for punishment technically, but the promise is there and I'd like to see it work!