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All topics get included in any output, regardless of whether or not they are in the TOC. To exclude topics you need to put a conditional tag on them and when you generate, create a build expression of NOT whatever tag you applied.
Thank you so much!
Just to confirm... So, that means all the generated files from the WebHelp/FlashHelp layout that reside in the \\RoboHelp 6.0\(projectname)\!SSL!\(layoutname) folder on my drive does not include the selected conditional topics?
When you generate the output, it will contain just those topics not excluded by the build expression.
If the different layouts you need are fairly constant, this 20 for one build, this 30 for another, all for yet another, you can set up multiple layouts each pointing to different target folders.