[stumped]

ticked is
all the manifest (3) and adobe (4) options, plus strip spans, insert or replace cover, update metadata, fix broken toc, broken images

its an issue only when the correct file name sequence for reading the book is not what you get with an alphanumeric sort.

i suspect its because of underlying structural issues in the epub, i just tried a calibre epub to epub conversion on the same problem book and that also shuffles the chapters into a wrong order.

i think changing my workflow may be simpler than trying to debug this

e.g. the chapter 2 file was created via a manual split so its called Section0002 it gets shuffled to below all the unaltered chapter files. and text/titlepage.html get moved to below that, because it comes after s ?

ps I am viewing the book in sigil, and checking content. opf and toc.ncx files before and after running the plug in.
I can see that the plugin changes the chapter sequence as specified in those 2 files, and makes it match an alpha sort of the xhtml file names

i have also used the plug-in for years, all OK, but twice recently I've hit this and both time its when trying to fix up and old poor quality sources so that they have well behaved chapter navigation once converted to kepub and viewed on kobo

the common factor seems to be that I need the navigation to follow the file sequence as laid out in book browser (left column of sigil view) , and not to impose an alphabetical order.

all i want to be able to do is use merge files, or split at this point to make it one chapter per file, with one header per chapter, where the source has chapters spread over multiple files and/or multiple chapters within one file. then auto fix the toc to match that structure

so what the best current tool/workflow for that please.