I have endnote 4.0.2 on a macbook and I noticed that despite the style being (Author, Year), the year was not visible. I entered edit citation and the exclude year box is ticked on every reference. I would go through and change this manually but there are 400 references and there must be an easier way! I went to edit preferences already and the formatting boxes are unticked.
A way you should be able to fix it for this document, is a legacy setting in the preferences under formating. Untick the box that says “Omit Author or Year from formated citation if …” Unformat and reformat, and they should reappear in the formated document. (Many years ago, I asked for this box, so I could just type in my record numbers before the add-in was so flexible!)
I have heard this happening over the years, but don’t know why or how. Does it also happen on newly constructed documents? If so, maybe tech support is aware of what might cause it in the first place.
One way to fix it more permanantly, if it has only happened in the one document, which would also restore your ablility to omit one or the other in random refs, would be to create a new style that has [Author, Year #Record Number] in the citation template and no bibliography templates. With the tickbox described above unchecked, format A COPY of your document with this new style. Select all and remove field codes (on a PC, this is Ctrl+shift+F9). Now reformat the document with your preferred style, but change the temporary citation delimiter brackets in the dialog box to square brackets. This should create the correctly formatted document. You can reformat once more and return to curly brackets if you like, but it isn’t necessary.
Since I tested the above, I attach a squarebracket, citation only style you could use.
added in edit: Oh, and don’t forget to put the formating preference back to checked, if you do ever want to omit year or author!