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in calibre right click on the book, then click on edit book. The book has to be epub or azw3 format. Once in the edit of the book then at the top is the tools menu, from there Edit Table of Contents.
As for as edit the TOC that is something that I just had to figure out. If the book has a TOC but it is not pointing to the correct files then it is just going down the list and pointing them. I the ones I did there was a TOC and the pointers where missing so I clicked on the correct the TOC and followed down the files to find the correct ones. It is slow but can be done with some practice.
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