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This happens if you have previously built TOC with Process numbering in decimal notation set, but then have rebuilt it without numbering. In such situation you need to clear all HTML code inserted with Menu > TOC > Clear TOC and all HTML code inserted keeping all previous settings in force, then change settings to new and rebuild TOC.
This happens because if Process numbering in decimal notation is switched off, then program doesn't deal with numbering [doesn't make an attempt to recognize it].
Because program finds existing named anchors [that actually were built previously by the program], it doesn't change them. It generates named anchors only in a case of their absence.
You need to clear previous results by using Menu > TOC > Clear TOC and all HTML code inserted first, and then build TOC with new settings. Named anchors will be re-created with the new attributes.
Just include it into the list of source files. Even if you check Insert local TOC into each source file, local TOC inserted will be overwritten with common TOC for all source files.
This is because numbering is always inserted right after the header tag, while other header text is usually inside named anchor. To make sure that they have the same style, set properties of <h> tags and named anchors to be the same.
See also: Where numbering is inserted
Take those files of a project where you need the numbering in the headers and according TOC items and build TOC with Process numbering in decimal notation set. Append the rest of the files, which you don't need to have any numbering. Rebuild TOC again with Process numbering in decimal notation turned off.
If you put <!-- TOC --> tag somewhere, all headers prior to this tag are not handled by the program and not included into the TOC.
If you need to exclude some header in the middle of the text, then change its importance, say from <h2> to <h4>, and change the range of the headers processed so it falls outside.
It is easy. There is the level variable that you can use to provide different class attribute to items from different levels. Example:
<li class="toc_item_<!--#echo var='level' -->">....</li>
We have prepared a style named Bulleted tree with "differentiated" headers for you to handle this situation.