Hi David,
I fear that this is one of those situations where it’s impossible to predict the best outcome. Ideally you would be let in to catch the replacement train, but if that doesn’t happen then you’re not going to avoid some sort of dicussion. You haven’t said where you were going to and who ran the trains out of Paddington (EL or GWR)?
The middle journey has been separated out because it was incomplete. I would have hoped that the helpline would listen to your story and match the touches with what happened. I’d be inclined to try again, and ask to be escalated to a manager if they still say no. If you’re still not getting any joy then email to custmer services with the full story again and ask for either a refubd, or a deadlock letter so you can take it to the ombudsman.