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The metadata editor just changes information in the Calibre database - it does not actually modify the ePub file.
If you want to insert a cover into the ebook file without any modifications then the easiest way is to use either the Calibre "Polish Books" function or the "modify ePub" plugin.
The fact that the "Save to Disk" function did not insert the new cover means that the original epub file had no identifiable cover to be replaced. Both the Polish Books and Modify ePub methods would correct this.
Another option is to use the Calibre edit book function as that gives you complete control over the contents of the epub file.
Conversion always makes changes so do not use that if you want the original css styles and names to remain intact. This is just the way that the Calibre conversion pipeline works and is not amenable to change.
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