I ran into the same problem after switching from my old MacBook to my new one. Up until then Pages and EndNote went together just fine and I had no problem getting my in-text citations in a number (e.g. (2)) format while my bibliography was displayed in Vancouver style.
Now it it stuck on the Autor-Year format, not matter what I do. I tried your advice, changed the citation template “Citation” to (Bibliography Number) and even the “Citation - Author (Year)” displayed below that into the same format for good measure. Saved the style, made sure to switch to the new style in Pages - Pages just keeps on displying all in-text citations as “Author-Year”. I even went back on my old computer to see if the settings where somehow different there but they are exactly the same
I’m all out of ideas and would be extremely glad for some help.
Yeah I am using the most recent version of both the plug-in and Pages, the latter seems to be the actual problem. I just found another user complaining about broken in-text citations, I suppose I’ll just wait for the next update and hope for a bug fix. Worst case, I’ll downgrade to Pages 6.1 or even 5 as all was running fine with those.
Very annoying but at least I know what the problem is now.
Do you use Endnote online with a institution with a site license? The librarians there, might be able ot help you, if so. Otherwise I am still not aware of any tool to view the online style formats for a similar superscripted style.