The log has the following lines:
Quote:
DEBUG: 0.0 KoboTouch:books - driver options= Driver:KoboTouch, Options - format_map: [u'kepub', u'epub', u'pdf', u'txt', u'cbz', u'cbr'], use_subdirs: True, read_metadata: True, use_author_sort: False, save_template: {author_sort}/{title} - {authors}, extra_customization: [], manage_collections: True, collections_columns: series, create_collections: False, delete_empty_collections: False, ignore_collections_names: , upload_covers: False, keep_cover_aspect: False, upload_grayscale: False, show_archived_books: False, show_previews: False, show_recommendations: False, update_series: True, update_device_metadata: True, modify_css: False, support_newer_firmware: False, debugging_title: , driver_version: 2.3.1
DEBUG: 0.0 KoboTouch:books - prefs['manage_device_metadata']= on_connect
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The first line shows the driver configuration. The highlighted bit shows that you have collection management enabled. And the series column is being use for the collections. But you don't have the options enabled to create new collections or delete empty ones.
What that means is that when you connect the device, the driver will do collection management. In this case, no extra collections will be created, and empty ones will be left. But, the books will be removed from all collections that do not match the name of the series they are in. And that means that any book that is not in a series, will be removed from all collections it is in.
This is what I was expecting to find. The driver is working correctly, and is doing what you have configured it to do. If you don't want the driver to do the collection management, you need to deselect that option in the driver configuration.