@robin58 - you can look inside the opf files with a text editor - its rebadged xml.
I have this at the end of all my opf's - even if there is no cover
Code:
<guide>
<reference href="cover.jpg" title="Cover" type="cover"/>
</guide>
I just did a test with goodsynch 9.7.9 and calibre 1.24. I forced a bulk change on my Test library, updated metadata on a couple of 'books' I'm editing and added 3 journals - no surprises, only see the synchs I expected.
BR