in xslt2, if I understand you correctly something like

<xsl:variable name="a" select="/"/>
<xsl:variable name="b" as="item()*">
  <xsl:apply-templates mode="a" select="$a"/>
</xsl:variable>
<xsl:variable name="c" as="item()*">
  <xsl:apply-templates mode="b" select="$b"/>
</xsl:variable>
<xsl:sequence select="if(deep-equal($b,$c)) then $a else $c"/>


In the above I have  understood 

> If the second stylesheet  doesn't match anything 

to mean that it returns its input unchanged (which means that it must
havehad at least a default template matching everything) If you really
don't match anything so the result of the second transformation is empty
then change the last line to

<xsl:sequence select="if(empty($c)) then $a else $c"/>

David