RE: overwriting certain blocks of output - two queries
input.xml (call to first.xsl) --> first.xsl (some processing) --> first.xml (use saxon:next-in-chain) -->second.xsl (target certain o/p areas of first.xml) -->second.xml (final result)
I'm not qualified to speak to next-in-chain, but from hearsay it should address what you want. Howeve, note that in principle interim output need not be serialised as files--they could just be held in memory and fed to the next stylesheet in chain.
Note that there's no notion of "overwriting" things -- the interim output, fed to the next stylesheet in chain, is, for all it knows, brand new input, for it to preserve or munge as it will. Stylesheets after the first could refer to the original input (via document(), for instance), but the chaining business simply obviates the need for a separate, controlling application.
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