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I think what would work seamlessly for this case is to make one more extension to this feature - have Calibre write an MD5 hash to the database for the documents when they're added to the DB, and updated any time Calibre manipulates the actual file. If a format->format conversion will overwrite a hash that matches the database then commit the conversion without prompting the user. If the hash doesn't match then this is an indicator that the user did some outside manipulation to the file, and this could then prompt a warning/selection choice to click through.
That way the majority of the users never have to click through a confusing screen, and power users don't need to worry about accidentally destroying work done outside of Calibre.
This hash idea has been discussed before in part to accomplish some of the things this backup feature is trying to accomplish, perhaps it's a bit more relevant to add now that this new functionality exists.
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