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@BelgarionNL - if you are new to the plugin your books in calibre do not as yet have a goodreads_id identifier. The plugin has to know which book in calibre maps to which book on your shelf (known as "linking" the books). Once the books have been linked, you don't need to do that step again for a particular book. You can see the goodreads id for a book in the edit metadata dialog (or can display it as a column - see the first post in this thread).
There are various ways of linking books - either via that dialog as you are doing, via ISBN if it is present on the book (and matches your shelf), via the Link book option on the Goodreads Sync menu, or via the Goodreads metadata download plugin. All have slightly different purposes/uses.
It sounds like your starting point is that you have a Goodreads account already, have a bunch of specific editions of books on it, and now want to sync that up against your calibre library. Since you have already chosen a particular goodreads edition to be on your Goodreads shelf, that must now be reconciled with whatever edition you have in your calibre library, and frequently the numbers may not match up (requiring your one-time manual intervention on that dialog). Could be different ISBNs or goodreads ids even if you did have the latter from the metadata plugin.
If however you were like me and had no books on your Goodreads shelves (new to using Goodreads website) then I instead use the "Add to shelf" functionality of the plugin. If you have used the Goodreads metadata download plugin it will have chosen a goodreads id for the book for you. So adding to a shelf then usually involves no double clicks to link ids, and any future syncs from that shelf are also linked. Even this approach is not perfect though - it might be that it is not the edition you want showing on your goodreads shelf (maybe it has no cover, is missing page information or whatever) and so then you need to manually re-link it and update your shelf edition appropriately.
Hope that helps...
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