I did eventually solve this - with no help whatsoever from the N6 user manual!
I tried every combination of the available options and eventually found out that it was necessary to set my hardware back to 48kHz then UN-Freeze all VST Instruments and then save the project and exit the program before resetting the system to 44.1kHz, restarting N6 and going through all of the Sample Rate Adjustment options until I happened upon a combination that worked - that was the day done.
Searching through the PDF user manual (which is not kept up-to-date by Steinberg when updates are released - so all of us have out-of-date manuals) I could find no references at all to any of the options that come up when attempting to change the sample rate of a project when launching the program.
Could somebody from Steinberg please update the user manual with appropriate documentation? - It will be a benefit to you (fewer support calls) and the users (no more stabbing in the dark all day long).