I installed calibre-web from
https://github.com/janeczku/calibre-web, and that's all I need to keep my library in sync with my kobo.
Calibre-Web is a web app providing a clean interface for browsing, reading and downloading eBooks using an existing Calibre database.
It allows multiple accounts, shelves, file uploads, format conversions, and new features include kobo sync, with kepub encoding on the fly.
You only need to enable the kobo sync option on the admin panel and some small fixes in eReader.conf, changing the api_endpoint to a token provided by the app (with your server ip). More details in
https://github.com/janeczku/calibre-web/issues/1470
They're working on a method to sync only a part of the library, in case you have a very large one.
I'm running it as a container (from linuxserver) with zero problems.
Any questions / thoughts?