@Noughty - I will be honest and say I have not the foggiest idea what you are trying to achieve, but it sounds complicated
. I don't use any Goodreads shelves other than the standard ones so it is out of my familiarity zone.
In my ignorance I always saw all that behaviour as mutually exclusive. You choose one side to be your master and you stick to it. Either you start from having a Goodreads account with lots of shelves that you want to populate in Calibre (and continue to update in that direction, or after the initial pull from that point on you do updates in Calibre and push to Goodreads). Or you start with a Calibre collection and push all your updates to Goodreads.
From what I read above you are trying to push and pull from Goodreads on an ongoing basis, which sounds like a recipe for conflict and complication to me. But then as I said above I don't understand exactly what it is you are trying to achieve?