Hi, thanks for your suggestions.
I tried a number of things to resolve the problem in Word, including resaving the document and accepting all changes - it had quite a few tracked changes. This solved my problem in Word, however, I then had a message in EndNote: Generic Error. I got rid of this by switching to an author-date style. Eventually I managed to get Vancouver to work. I altered this style to superscript the in text citations - on a couple of them it grabbed some of the text in the document and put that into superscript as well. I fixed this manually in Word. I have my fingers crossed this document won’t need any further editing, it was rather stressful.
Thanks again.