Migrating glossary xsl code to main xsl----which copies source xml to
outputxml with Updates of glossary elements in outputxml, but getting output
with no contents in divisions. Except glossary. What changes will required?

As per the XML you posted lasted, this template looks unnecessary (or
you have something else also in the XML).

<xsl:template match="*">
   <xsl:copy>
       <xsl:copy-of select="@*"/>
       <xsl:apply-templates/>
    </xsl:copy>
</xsl:template>

Regards,
Mukul