Running some stats on the <dicteg>s, ECH discovered that a bunch of data is missing from these tags in the rescued.xml file. Tracing back through the original process I followed (and thankfully documented carefully here), it seems that the data was discarded unintentionally during the final phase:

• Ran rescued_empties_removed_expanded_fixed.xml through collapse_forms_etc.xsl to produce rescued_empties_removed_expanded_fixed_forms_collapsed.xml.

This process changed data that looks like this:

<dicteg>
                     <cit>
                        <quote>√yə́ʕˀʷ+yəʕˀʷ‐t sn̩cʼələx̣ʷqén<gloss>*strong whirlwind</gloss>
                        </quote>
                        <bibl>JM2.194.7</bibl>
                     </cit>
                  </dicteg>

to this:

<dicteg>
                     <cit>
                        <quote>
                                 <seg><gloss>strong</gloss> whirlwind</seg> <bibl>JM2.194.7</bibl>
                        </quote>
                     </cit>
                  </dicteg>
      <dicteg>

This can be remedied by re-running that final step once I've figured out the problem. Since rescued.xml was created, it has been edited, but only to the extent of deleting about a dozen entries which have been confirmed as dupes or migrated into the main files; it should be easy to discover which these are and remove them.

The problem seems to lie with these two bits of XSLT, although I can't actually see what's wrong with them:

<xsl:variable name="tagFirstTextInQuoteAsPhr" select="true()"/>

<xsl:for-each select="./node()">
      <xsl:choose>
        <xsl:when test="self::text() and not(preceding-sibling::node())">
          <!-- Wrap the first text node in a phr tag.     -->
            <xsl:if test="$tagFirstTextInQuoteAsPhr = true()">
            <phr type="n"><xsl:value-of select="."/></phr><xsl:text>
            </xsl:text>
              <!--Append any <bibl> which is a following-sibling of the parent <quote>.-->
              <xsl:if test="(parent::node()/following-sibling::bibl) and ($moveBiblIntoQuote = true())"><xsl:copy-of select="parent::node()/following-sibling::bibl"/><xsl:text>
              </xsl:text></xsl:if>             
            </xsl:if>

        </xsl:when>
        <xsl:otherwise>  
          <!-- Apply templates to everything else. -->
          <xsl:apply-templates select="." />
        </xsl:otherwise>
        </xsl:choose>
      </xsl:for-each>