Regarding Automation: Using the instructions
from here, I made the plugboard below. Noticed though that the recommended setting for Metadata Management is to use "Automatic Management", but I've set mine to "Manual Management". I wonder if that's causing the issue.
I don't have duplicate shelf names under "My Collections". I used the KoboUtilities plugin to verify this.
But I noticed that once in a while, when connecting my Aura to Calibre, the series tags of some books in the device gets deleted. I then have to delete the book from the device and re-send it to fix the problem.