I suspect that your “default” output style (which is not specifiable in any way I know) is currently set to something like “annotated.ens” in each of your new and existing documents.
Changing the output style in Endnote has no effect on this behaviour. – If you change it to your needed output style (say Author, Year) on the endnote ribbon (in Word 2007/2010/2013) or in the format Bibliography dialog (in Word XP, 2003 and 2011), this will restore your citations.
Also eventually, it does seem to become the “default” for new documents, but I have no idea how and when.