My advice for the quickest and best way to resolve the problems is to arrange a site meeting with your architect and BCO to discuss and resolve the issues. There's possibly more then you've realised.
Take notes at that meeting 'cos you probably won't remember it all.
List the items for discussion and list the resolutions.
BCO won't mind and it won't cost you anymore.
Architect should have built contingency in fees.
Thats fine and i have done that, BC application only just gone in as planning just passed last couple of days.
The main concern was that i would have to fit a new external soil stack because i would have to re-run all my internal waste pipes to it. Creating more work and more cost.
Is a solution possible without having to install a new external soil stack?