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Originally Posted by travger
I hope to learn how to keep such things out of my library. When I moved it, apparently every folder and opf was copied and left behind.
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This problem doesn't arise because of library/calibre issues. It arises because by using 'copy', the backup folder hierarchy is the union (a merge) of everything that has ever been in the library since the first copy.
Assume you make a copy today, and that the book The Doom of Horseflies is in your library. Tomorrow you delete the book, and the folders etc are removed from your library. You then do another copy backup. The book is not in your library and therefore won't (can't) be copied, but it is still in your backup because it was there yesterday. Your horseflies are still doomed.
There are some situations where a merge is exactly the behavior you want. For example, assume you keep 12 months of bank statements on your primary disk, but all bank statements on your backup media. Using copy would be appropriate, because removing older bank statements from your primary storage should not remove them from the backup media.
One must decide between backup and archive. A backup is a copy of something that can be used to recreate (easily) the original. An archive is a collection of data that is (usually) a superset of the original. Both schemes have their place.
(Apologies if I am explaining something you already know. I do tend to get pedantic.

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Thanks on the tip on the synchronizers!
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You are welcome.