@Italophile and @Charles Kenyon:

Thank you both for leaping to my aid. Since posting my message, I discovered the solution to the problem.

I closed down all instances of Word, and then reopened the main document. All the formatting was retained and correctly applied. I then tried updating the TOC and the Index and this time they both worked perfectly.

I've no idea what goes on in the background, but this seems to have required a complete close for it to work.

Just in case anyone is reading this and would like one quick tip too... I found that there were several timeout errors subsequently as the files were stored on One Drive. Moving them to my PC (not just available through OneDrive) resolved this too.

Thanks again, Graham