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This question was posted in response to the following article: http://help.adobe.com/en_US/robohelp/robohtml/WS454F21D1-1010-4fa6-99D4-BF9163E4D78C.html
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Is there a difference between applying a conditional tag to a TOC topic (select a topic in the TOC and apply tag) and applying it to the topic itself (Select the topic from the topic list or select the condition option in the topic properties.)?
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Yes there is a difference. If a CBT is applied to a TOC topic, the topic will not appear in the TOC but (and it is a big but) the topic is still included in the output. It will be searchable. If a CBT is applied to a topic (e.g. via the topic list pod) it will not be included in the output and therefore also not in the TOC.
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I thought that might be the case. Thanks!