Thank you so much for taking the time to look into this little issue.
After doing a little bit of quick reading, I renamed one of my epub files to .zip and peeked at the file structure. The ePub format is far simpler then I had originally imagined, although I don't pretend to fully understand the relationship between all the files.
If I understand correctly, however, the cover image is stored in the same folder as the document files and I assume that one of the files specifies the name of the image file to use as the cover.
My problem would have been avoided completely if calibre had a "replace cover art" function avoiding the conversion from epub to epub.
At any rate, thank you for your help.