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When metadata is updated in calibre, it only updates the cali8bre database, not the books themselves.
There is a special Embed Metadata feature which will update the in-library copy. "Polish Books" ca do that as well.
Conversion from one format to another uses the current library metadata when creating the new ebook file.
Using Save-to-Disk by default performs an Embed Metadata on the exported copy (the one you saved on your Desktop).
Save-to-Disk also by default saves a copy of the Calibre Library cover as Booktitle.jpg, and an XML representation of the metadata as Booktitle.opf
calibre does not know or care what an "Apple Cover" is.
The only cover that calibre cares about is the cover image specified according to the official EPUB specification, or the documented cover image from the AZW3/MOBI/etc. formats.
P.S. You cannot update the cover inside a MOBI file once the MOBI file is created. You need to decide on an image before you create the MOBI.
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