I found a bug...
Code:
calibre, version 1.39.0
ERROR: Modify ePub failed: No ePub files were updated
Modify ePubs
Logfile for book ID 12248 (The Silver Spike / Glen Cook)
12248
Modifying: C:\Users\Jon\AppData\Local\Temp\calibre_2aeddf\onhui4_modify_epub\12248.epub
Parsing xml file: OEBPS/package.opf
Parsing xml file: OEBPS/toc.ncx
Looking for broken links in the NCX
Changing playOrder from: 0 to: 1
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ePub not changed after 0.22 seconds
That is a change to the ePub and it should allow the ePub to be updated. That was just using the option "Remove broken TOC entries in NCX file".