I would not agree that the parent message is a solution.
To summarise, after raising a ticket with Microsoft, we have come to the conclusion that the 'get notebooks' connector only seems to list whatever notebooks appear in the recent's list for onenote.
I am waiting for Microsoft to get back to me with a confirmation on this. Once I get it I will post something here. Microsoft suggestedthat I manually open the notebooks that I'm looking to process so that they appear on my recents list. My issue is that I need to open all of my notebooks. I didn't investigate this further, but I suspect the recent list is limited to 25 notebooks.
Anyway, I will post an update once I get something back from Microsoft.