As far as I can tell, it is not possible to format prefixes within in-text citations. If there IS a way to do this, great. If not, please put this on your high priority list, as this is a common need in scientific writing.
This is a restriction of Word’s “fields” and I don’t think Endnote can control it. You could instead opt to use custom endnote field and insert the endnote field in the output style, rather than a prefix – format the text in the endnote field.
But I just tested editing the prefix manually after insertion, and it stuck - unless I fully unformatted and reformatted citations. I was surprised it stuck even after adding other citations to the document.
Very oddly, I just formatted a prefix in a test document, and it also remained after updating citations and even after adding more citations, although NOT if I add a second citation in the same in-text parenthetical. That is, “(italics-citation)” remains the same if I update, even if I add a later citation (e.g., “text (italics-citation1) more text (citation 2)”. However, if I add a second citation to the first parenthetic— e.g., “(italics-citation1, citation2)” — then the italics reverts to normal font. However, if I then re-italicize the text, this remains italicized after updating.
Hence, it appears that the culprit here is that I cannot add a second citation without re-formatting the key term.
In my experience this has not seemed to be the case (I kept losing italics) but I will pay closer attention. Thanks for the feedback!!