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@JoonieB - my solution to this was to just turn off the "Comments" downloading for the Amazon plugin. So you will still get other "things" made available, such as covers or ratings data, but the Goodreads comments can never be replaced by Amazon ones.
The only situation in which this can cause an issue is for a book in Amazon not in Goodreads. In reality this happens so rarely as to not be an issue (Goodreads database is built from Amazon plus B&N plus other sources, so it is arguably much better than Amazons own!). The only time you *can* have a problem is if the ISBN grouping match comes back with Amazon in an ISBN pool of its own. This is when doing single metadata downloads via the Edit Metadata dialog is best, because you can pick the Goodreads result manually (and if necessary do a second download metadata to pickup the Amazon id, but comments will not get overwritten).
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