The problem is that most people do NOT want all books in their Calibre library synce'ed to their reading device. This can be either because they have more books than they have space for on the reader, or simply that only a small selection is needed.
One thing you could do is use the Calibre facility to auto-add a tag to new books when they are added. This helps with identifying new books that you want to sync that are not yet synced. If you combine this with the Reading list feature for removing a tag on syncing then you should get most of what you want with minimum effort.
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