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.