[JimmXinu]

I dunno--you're using features I've never used and I didn't write it, so...

The relevant block of code appears to be:

Spoiler:

    def _rebuild_auto_device_list(self, db, list_name, on_device_ids):
        if DEBUG:
            prints('READING LIST: Auto-populating device list: ', list_name)
        existing_book_ids = set(cfg.get_book_list(db, list_name))
        ids_to_remove = list(existing_book_ids - on_device_ids)
        ids_to_add = list(on_device_ids - existing_book_ids)
        if DEBUG:
            prints('READING LIST: Removing %d ids from automatic list: %s' % (len(ids_to_remove), list_name))
        self.apply_tags_to_list(list_name, ids_to_remove, add=False, modify_action='TAGADDREMOVE')
        if DEBUG:
            prints('READING LIST: Adding %d ids to automatic list: %s' % (len(ids_to_add), list_name))
        # We will force the apply of tags to ALL items on the list, just in case the user
        # has only just specified a tag.
        self.apply_tags_to_list(list_name, list(on_device_ids), add=True, modify_action='TAGADDREMOVE')
        cfg.set_book_list(db, list_name, list(on_device_ids))
        ids_to_remove.extend(ids_to_add)
        return ids_to_remove

The code is explicitly ignoring the list's setting for modify_action when it's an auto-populated list.

That's the only place in the RL code that the apply_tags_to_list(...,modify_action=...) parameter is used, which suggests it was deliberate? (Interestingly, search populated lists explicitly disable updating column/tags from list.)

I think it would do what you want if the modify_action='TAGADDREMOVE' parameters are removed.

Attached is a version with that change. I haven't tested it -- use at your own risk and test it first.