
The plugin community is the best!
So after many hours of tinkering and with the amazing help of Claude.ai I think I'm in a place I'm happy with.
My ebooks are stored on my Synology which Calibre Web Automate runs on. I then put syncthing on, Claude wrote a script that runs daily which copies these books to a flat structure that then synce to my Kobo when I'm on wifi to push any updates and keeps them without subfolders.
It also made a script to correct and move over the series data as I found that wasn't pulling through.
It does mean on my Synology I double up my ebooks but I have the space (but I have plenty) so now I have Bookshelf running with various other pluggins but it world seamlessly.
Kobo is so good for tinkering when KOReader is on it.
Thanks so all the people that make these amazing plugins!