Thank you both for your comments.
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Originally Posted by banjomike
I don't see how you can have an option which allows users to maintain their own collections and still have Calibre put collections back when it notices thay have gone. #2 seems to be the closest to what you described in post 1.
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The thought was that by putting something in the collections box, the user was asking calibre to ensure that the collections honored those metadata attributes. Seemed right at the time.
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Having said that, I will probably stick to letting Calibre maintain my collections.
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and
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Originally Posted by dwanthny
Seems reasonable to me, but I've unchecked Preserve device collections. 
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It is probably worth clarifying the effect of the proposed change if the option is cleared. The safest implementation (and I want to be safe at this point) will be for calibre to process collections at the same point (sending a book) regardless of how the option is set, but with different effect. If the option is cleared, when a book is sent, calibre will add any collections necessary, *and* (this is the effect of clearing the option) delete any collections no longer indicated by the metadata for that book. Collections will not be rebuilt at any other time.