If the filter is sufficiently simple just repeat it on the xsl:number
<xsl:number count="section[not(title='second section')]"/>
might do the right thing.
In general, you might find it easier to do do the transform as a
multi-stage process, first filter out (and re-order) the elements using
a "modifoed identity transform" then use this document as input to
a stylesheet that does the actual formatting.
For debugging it's often best to do this as two completely separate
processes (so you can look at the intermediate file) but there are
several possibilities (including the common node-set() extension to
chain the two transforms into a single process, which would be more
effificent.
David
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