<xsl:value-of select="$nameStr"/>
value-of returns a text node with the string value of its argument so
you lose all the markup, you could use copy-of instead, or more simply
get rid of the variable and just do
<affil id="{label}">
<xsl:apply-templates/>
</affil>
You haven't shown enough code to be sure but you may still lose the
markup
if you have added the replace() function in a template matching aff
replace() is a string valued function and you don't want to convert the
entire content of aff, to a string, you just want to process it's text
nodes, so
<xsl:template match="aff/text()">
<xsl:value-of select="replace(.,___,___)"/>
</xsl:template>
<xsl:for-each select="//aff">
are you sure you want // there (which means search the entire document
to arbitrary depth)
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