Are unindexed fields stored seperately from the main inverted
index?
        If so then, one could implement the field value change as a
delete and
        re-add of just that value?

The short answer is that won't work. Field values are stored in a
different data structure than the postings lists but docids are
consistent across all contents of a segment. Deleting something and
readding it is going to put it into a different segment which is going
to keep this from working. (Not to mention that you want the postings
lists updated if you want it to be searchable ...)

        Are you aware of some implementation of Lucene that solves this
need
        well with a second index for 'tags' complete with multi-index
boolean
        queries?

I'm pretty sure this has been done, I'm just not 100% sure where. Does
Nutch index link text? I don't know if Solr has anything like this but
if I remember correctly, Collex has tags but as far as I can tell, it's
not been open sourced (yet?)

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