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@ecorbett: This is working pretty much as designed.
The collection management is done by the driver in calibre. It uses the values in one or more columns to add books to, or remove them from collections. The driver can also created or remove collections. This is designed to be one way. And it is intended to be done each time the device is connected.
The driver has an option to ignore specified collections. You have to enter the names of the collections to be ignored into the driver configuration.
The "Get Shelves From Device" in this plugin is not intended for frequent use. It was added more as a way to recover for some sort of problem. I think the final prompting for adding it was someone who somehow lost their calibre library and wanted to retrieve it from their Kobo device.
The "Get Shelves From Device" can be used with the driver doing the collection management, but, you need to make sure the columns used in the two places do not overlap. And that you specify the collection to be ignored by the driver. From memory, someone is using this to rate their books. They have a collection for each rating and add the books to these. These collection are specified in the driver to ignore. And they periodically use the get to get the ratings.
The other problem is that the collection management is intended to be done when the device connects. This means that any changes to the collection will be done before you can do the get. You could change the metadata management to manual, but, that would mean that metadata such as the series info is not automatically updated when the device is connected.
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