Preserving entity references when transforming XML with XSLT?

If you know what entities will be used and how they are defined, you can do the following (quite primitive and error-prone, but still better than nothing):

<xsl:stylesheet version="2.0"
 xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
 xmlns:xs="http://www.w3.org/2001/XMLSchema"
 xmlns:my="my:my">
 <xsl:output omit-xml-declaration="yes" indent="yes"/>

 <xsl:character-map name="mapEntities">
  <xsl:output-character character="&amp;" string="&amp;"/>
 </xsl:character-map>

 <xsl:variable name="vEntities" select=
 "'stackoverflow',
 'How can I preserve the entity reference when transforming with XSLT\?\?'
 "/>

 <xsl:variable name="vReplacements" select=
 "'&amp;so;', '&amp;question;'"/>

 <xsl:template match="node()|@*">
  <xsl:copy>
   <xsl:apply-templates select="node()|@*"/>
  </xsl:copy>
 </xsl:template>

 <xsl:template match="https://stackoverflow.com/">
  <xsl:text disable-output-escaping="yes"><![CDATA[<!DOCTYPE doc [ <!ENTITY so "stackoverflow">
<!ENTITY question
"How can I preserve the entity reference when transforming with XSLT??"> ]>
]]>
  </xsl:text>

  <xsl:apply-templates/>
 </xsl:template>

 <xsl:template match="text()">
  <xsl:value-of select=
  "my:multiReplace(.,
                   $vEntities,
                   $vReplacements,
                   count($vEntities)
                   )
  " disable-output-escaping="yes"/>
 </xsl:template>

 <xsl:function name="my:multiReplace">
  <xsl:param name="pText" as="xs:string"/>
  <xsl:param name="pEnts" as="xs:string*"/>
  <xsl:param name="pReps" as="xs:string*"/>
  <xsl:param name="pCount" as="xs:integer"/>

  <xsl:sequence select=
  "if($pCount > 0)
     then
      my:multiReplace(replace($pText,
                              $pEnts[1],
                              $pReps[1]
                              ),
                      subsequence($pEnts,2),
                      subsequence($pReps,2),
                      $pCount -1
                      )
      else
       $pText
  "/>
 </xsl:function>
</xsl:stylesheet>

when applied on the provided XML document:

<!DOCTYPE doc [ <!ENTITY so "stackoverflow">
<!ENTITY question
"How can I preserve the entity reference when transforming with XSLT??"> ]>
<doc>
    <text>Hello &so;!</text>
    <text>&question;</text>
</doc>

the wanted result is produced:

<!DOCTYPE doc [ <!ENTITY so "stackoverflow">
<!ENTITY question
"How can I preserve the entity reference when transforming with XSLT??"> ]>

  <doc>
      <text>Hello &so;!</text>
      <text>&question;</text>
</doc>

Do note:

1. The special (RegEx) characters in the replacements must be escaped.

2. We needed to resolve to DOE, which isn’t recommended, because it violates the principles of the XSLT architecture and processing model — in other words this solution is a nasty hack.