Problem with Bibliography in Master Document


I have formulated a Master document with subdocument links for my research thesis and am having trouble formating the bibliography.

All the references in my master and subdocuments are unformatted as per instructions and all the subdocuments expanded.

When I go into my master document and go to Tools-endnote 6- update citations and bibliography- Endnote starts to do it, then times out with an error message- something like 1725. Then word freezes and I have to force quit word.

I’m not sure what is going on. I want to add the reference list at the end of the conclusion which is in the master document and have the subdocuments ( All my appendices) as separate documents - but I need the reference list in the master documents to talk to the subdocuments as the reference style is Vancouver and if they don’t link up the number order of the references in the subdocuments will be wrong.

Any help would be greatly appreciated.

Many thanks