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Nothing has changed in this version of the plugin as far as how metadata is updated. If you are seeing a different behaviour I believe it is because (a) you are now seeing an ISBN being extracted where it was being missed previously (due to the change I made), and/or (b) you are also using a different calibre version.
I don't see this behaviour myself, and it is impossible to guess if you don't actually include log file output, calibre version and do some basic testing yourself - does it happen for all books, is whether they currently have an ISBN relevant, is it epubs or PDFs or both etc.
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