Offhand can think of 2 possible situations where this might occur:
1. The Endnote citations and bibliography were accidentally converted to plain text. (Could you check to see if the citations/bibliography are still connected to Endnote - just place your cursor over a citation and see if changes color);
2. If Track Changes was used while the document was in “Final Show Markup” mode and with CWYW turned on this has the potential of corrupting existing citation field codes during the updating process .
In both cases, the only way to reactivate the prior references is to reinsert them into the document.