It is likely that you unformated the references,which turns off Cite While You Write (CWYW). Turn it on again from the Format Bibliography option on the toolbar or in the Word, tools, endnote tools> format bibliography option. – it will be on the third tab.
(updated X7 and X8 – the option is now on the Endnote ribbon -( a toggle “Instant formating is ON” or “is OFF” and you don’t need to go into the bibliography menu). You can also manually “update …” when ever you prefer, if it is “off” – just remember to do so before submitting! )