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Originally Posted by Otter
But what do you mean by "current metadata"? The collections currently beside each book in calibre's main library view?
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Yes. "Metadata" means all the metadata stored by calibre with a book. "Current metadata" means the metadata in the library (not on the reader) at the moment the device is connected.
Manually-added collections are names that do not correspond to a value in one of the metadata fields selected in 'device customization' for collection generation. The default is series & tags. Assume you used the Sony SW or calibre's device view to add 'Foo' to the list of collections for a book. If metadata management is not 'Manual', and if 'Foo' is neither a tag on the book nor the series the book is in, then the book will be removed from the 'Foo' collection. If at the end no books are in the Foo collection, the collection itself will be removed.
You could 'try before you buy' by making a backup of the Sony memory, running calibre, changing the option, then plugging in the Sony. If you don't like the results, restore the Sony memory. If you have an SD card, you must back that up as well. If you decide to restore the Sony's memory, be sure to reset the option *before* you plug the device in again.