generate the comment delimiters <!--
and --> as text using disable-output-escaping or character maps; you
can then generate the elements as real elements.

Thanks Michael for suggestions. I will look into this. I need to
restore these elements as comments (I thought that will be best way)
as I need to re-transform back to the original.

This sounds as if you need to restore the elements from the comment
strings when doing the re-transform. Maybe it's easier to move the
elements you don't want to another namespace and than have something
like a pass-through template for that namespace:

    <xsl:template match="ignore:*">
        <xsl:apply-templates select="*"/>
    </xsl:template>