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See also: Building a table of contents in the Jutoh manual
Sometimes you may wish to incorporate several books within your project, as a box set, each book having its own table of contents, and also a master table of contents.
If you supply unique section headings for the top-level (title) page of each sub-book (or TOC for each book), such as Book Title then you can use the TOC wizard to use those headings, and if you want to create a gigantic master TOC then you can get the TOC wizard to recognise deeper headings such as chapter headings. So in this case, you can tell Jutoh to look for book title headings for TOC level 1 items, and chapter headings for TOC level 2 items.
Jutoh supports multiple TOCs. If you click on "+" in Project Projects/Indexes/Contents, you can create another TOC (as many as you like). Click on Edit 
to edit the properties of a TOC, including Scan a range of sections. So, you can limit the part of the project to a given book (choose the first and last sections for that book). You will need to also remove the "toc" guide type for individual TOCs, apart from the first, or ereaders won't know which is the main TOC.
Before you add the TOC, or after, you can create a new section document for each of the TOCs, and then in TOC properties, set the section that will be used for that TOC.
The first TOC in the drop-down list of TOCs is considered to be the main (master) TOC.
One potential problem is that if the master TOC points to headings within sub-book TOCs, the TOC bookmarks will replaced with new (different) ones when the sub-book TOCs are regenerated, causing the master TOC to point to missing bookmarks. However you could manually edit the master TOC to remove the anchors (to point to the files only) which should work in HTML-based formats, but not ODT. Or, you could ensure that the master TOC does not point to any sub-book TOCs by not including the TOC Heading style in the styles to be searched for by the master TOC.
If your master TOC only points to the top of the secondary TOC (using the standard 'tableofcontents' bookmark), there should be no problem.
Contents | Start | End | Previous: KB0086: There is an XML parsing error when opening a section | Next: KB0088: How do I add a clickable email address?