Open the file in epubfixer select edit table of contents press add. On the next page you should get a lot of selection boxes select them all and press add. Now you have a TOC but it is not named properly. The first few links would be to map and copyright page etc you can delete them or keep them and rename them its up to you I usually don't keep that stuff in the toc.
Then select all the toc link right click and press rename write chapter 1 use the check boxes and press ok. It should rename all the chapters from 1 to whatever is the last chapter.
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