To check what you are saying: there are shelves on the device that have books on them that are in the current calibre library and these shelves were not copied back to the column you selected?
And by "brought in all of the Metadata tags for books", what exactly do you mean? "tags" is one of the metadata columns in the library. Did you previously have this as a shelf column?
To help me understand what is happening, can you run calibre in debug mode and do the get the shelves and post the log? If you have a lot of books on the device, it will produce a lot of output, so it is better if you attach the log.
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