problem with footnotes

I’m having a problem that I’ve not been able to solve.

I’m using three different Endnote libraries in the same Word document (Endnote X3 and Word 2007), and I’ve been doing so for months without any problem. Today, while I was trying to insert a citation, my Word document crashed. I restarted it and verified that the text was left unchanged but the footnotes were not: some are functioning properly but the majority has become regular text, that is, they are no longer connected with Endnote, they don’t update and there is no dark highlight when I put the cursor on top of them. Also, for some reason, some of the footnotes became gigantic lists of the same citation repeated over and over. What is this? Can anybody help me get this document back to normal?