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calibre does not check if the cover is the same. That would be a waste of resources, with lots of false negatives since cover images are often resized. For instance, they are resized when added to calibre if larger than the max allowed size.
And the sentence is correct. Only if the original cover image can be indentified, can it be replaced. Otherwise, a new cover image is created and marked as the cover.
Although, since you are using a Kobo it might be that the Kobo driver (or kobo extras plugin) does something special for epubs. The way to test that is to use save to disk in calibre and see what happens to the cover in the saved epub.
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