> So far, I have been capturing the content of <p> in a string

don't do that, do this

<xsl:variable name="string" as="xs:string">
<xsl:value-of>
<xsl:apply-templates mode="zap-note"/>
</xsl:value-of>
</xsl:variable>
<xsl:variable name="p" select="."/>

then you want
<xsl:template match="note" mode="zap-node">
 <xsl:text>@@@@@</xsl:text>
 <xsl:value-of select="count(preceding-sibling::note)+1"/>
 <xsl:text>!!!!!</xsl:text>
</xsl:template>

so your string is

"Some text.  Some more text, with a comma. @@@@@1!!!!!"


> and then using  two nested <xsl:analyze-string> blocks with regexes,
> which work nicely and  do what I want.

so they should work on the above string (if @ or ! are used to look up
sentence punctuation in these regex, use different marker characters,
you can use unicode private use characters for example)

Then currently in you probably have something like

<xsl:matching-substring>
<seq><xsl:value-of select="."/></seq>
</xsl:matching-substring>

do instead




<xsl:matching-substring>
<seq>
<xsl:analyze-string select="." regex="@@@@@([0-9]*)!!!!!">
<xsl:matching-substring>
<xsl:copy-of select="$p/note[position()=regex-group(1)]"/>
</xsl:matching-substring>
...



so at the innermost level you can put the notes back.


David


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