A colleague from the School of Conservation Sciences has pointed out that:
a number of editors of Archaeological Journals specifically request that EndNote is not used in the compilation of bibliographies of submitted versions of papers submitted electronically for publication. All coding and links have to be manually stripped out before typesetting - Endnote conflicts with the majority of professional typesetting programmes - the references in text get seen as "code" so are omitted meaning that all references have to be added into text manually
This refers to Cite While You Write (CWYW) which leaves code in Word documents that is usually invisible to the user. It is important to check with the publisher for any specific requirements. The following advice is offered from the EndNote Forum ...
Other publishers specifically request that embedded field links are removed. You don't have to avoid using Endnote! You just need to eliminate the links before sumission. Routinely, I use ctrl A (select all), shift+ctrl F9 (unlink fields) ON A COPY of the manuscript for submission. Alternatively, use the Endnote "tool" to accomplish the same thing (the one with a little arrow pointing straight up.
Some publishers now actually prefer to have Endnote imbedded links, as they convert them somehow to create their html version of the online document. So it is worth while to check on their preference. Leanne