title_body: fix spine order and file names based on toc.ncx
upvoted_answer: Possible solution (which worked for me):
  
  generate calibre's ToC(as html) from correct toc.ncx (if not arleady exist)
  unpack epub
  re-import only html toc,
  convert result to epub
  if order is incorrect yet again - check Calibre's HTML-ZIP importer depth-first/breadth first mode