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I did not have any issues.
Don't know if it makes any difference but I always download to the downloads folder and then install from there rather than part of the download process.
You could always uninstall iTunes and then install the new version and reconnect your iTunes folder if it is not automatically reconnected but if you are not happy doing that I suppose you could always "restore" to the previous version using windows backup and restore.
There appears to be separate but related issue in that Calibre 3.9 has removed support for iTunes sync. I have requested that this is reinstalled as we now have this new version of iTunes that will not auto update but I don't know what will happen
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