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My guess would be that you are only going to be interested in books that still do not have an ISBN from the set that you scanned?
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Precisely... instead of only marking books where an isbn was found (isbn:updated) my idea was to mark books where an isbn was scanned for but not found.
Now that I think about it though... it is as murky as you thought. Since search parameters would start to confuse each other. I think my solution of a yes/no column is more elegant... if you could somehow change your plugin to create a yes/no marker... let's call it "Extracted" and mark those updated with a checkmark, and those failed with an x, that would be pretty elegant. By that logic, you could still have the option to view the updated isbns at the end of the job - and you could also leave the user the option to search on their own terms... for example "identifiers:false & extracted:false" would return a clean list of documents yet to be scanned.
If all this is impractical, though... I highly recommend my user-column solution to those that come after me. It's rather easy to search identifiers:false - highlight a selection - extract that selection - bulk metadata change the selection to true (then the documents with identifiers disappear from the list) - bulk metadata change the remaining documents to false - then do a search for customtag:true. That way, a search of identifiers:false can be sorted by the customtag column... the false documents would be easily identifiable.