Quote:
Originally Posted by At_Libitum
As far as I have used Calibre, the only times when it didn't extract the cover from the file is when it is not able to determine what the cover is, or if there is no cover in the file to begin with.
You could try the suggested bulk metadata edit method, as long as all other items are left unchecked, it will leave existing metadata unchanged. There will be an option at the bottom of the metadata editor (row of radio buttons) to retry that same action (extracting from file), but if that didn't happen the first time I don't know if this will work.
Question, where exactly do you not see the cover? Several places where it can be visible so before we are talking about different things think it might be helpful to know where 
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When you use the option to set metadata from the filename, it does not extract any of the ebook's metadata. You can still extract the cover in bulk edit, as was described, but when fresh from the import, the ONLY metadata that is set is whatever was explicitly set in the filename.