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The simplest way to avoid this is to use conditional tags. In the online version of your documentation - you'll have a heading in the TOC and the heading in the HTML file - and all is good. In the printed documentation, you will indeed have two headings - one for the book and one for the topic. So, what I do to avoid this is highlight the heading in the html file and apply a conditional tag - "online" - then I create a build statement for the printed documentation output that says "not online" and I end up with only one heading.
HTH
Paula
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Reading the other replies - I have one further comment. You can change the heading - but that is extra work and might confuse the end-user. More, it confounds QA...best, I believe is to highlight the heading and remove the duplication by tagging it as I previous wrote.
However - this is only in relation to the issue of there being duplicate headings because of the TOC entires.
If you are talking about duplicate topics - this also would be a result of the topic "appearing" in two places in the TOC. In this case, you can accomplish the same thing by tagging the TOC entry and appying a conditional tag, or building a separate printed documentation TOC and an output SSL for that.