It appears that KOReader does not handle a non-linear TOC very well. Both
Analog and
Asimov's magazines have recently changed (finally) their digital subscriptions over to epub and pdf files available outside of a particular vendor's application. The epub files they send have the content in the same order as the print version and the TOC matches the print as well. However, the TOC is grouped by section or length of story and is not sequential. This means that the chapter title and length are all wrong in KOReader, as well as the chapter ticks in the progress bar.
As you can see in the photo, in KOReader it shows that I am on a flash fiction story entitled "The Queen of Copies Meets Her Match" when I am actually on the top level section page entitled Poetry.
Is there any way to accommodate this unusual TOC? Perhaps leverage the file order in the spine of the .opf file?
I can always use Calibre to create a replacement TOC that is sequential, but I'm hoping there is a way for KOReader to handle this. The Calibre reader seems to handle it alright. In the screenshot below I am on the same page as the KOReader photo. Calibre is showing me in the correct section of the TOC. The chapter lengths and titles also appear correctly in the Calibre reader.