My PDF output had many blank pages in it. To enable filtering in the web help output, i had added MadCap:concept tags within the body of pages, for example:
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<html ....>
<body>
<h1 ....>
<p ....>
<MadCap:concept term="Definitions" />
</body>
</html>
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<html ....>
<body>
<h1 ....>
<p ....>
<div><MadCap:concept term="Definitions" /></div>
</body>
</html>