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The solution is to adjust the XPath of the following template.

This line ...

<xsl:apply-templates select="*[contains(@class, ' topic/topic ')]" mode="in-this-chapter-list"/>

... has to be changed to ...

<xsl:apply-templates select="descendant::*[contains(@class, ' topic/topic ')]" mode="in-this-chapter-list"/>

. The full template now looks like this:

<xsl:template match="*" mode="createMiniToc">
    <fo:table xsl:use-attribute-sets="__toc__mini__table">
        <fo:table-column xsl:use-attribute-sets="__toc__mini__table__column_1"/>
        <fo:table-column xsl:use-attribute-sets="__toc__mini__table__column_2"/>
        <fo:table-body xsl:use-attribute-sets="__toc__mini__table__body">
   …

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Answer selected by stefan-jung
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