Citations/References randomly changing

Citations/References are randomly changing in my thesis. I have a hard copy which I printed out, and the citations and references are correct. However, when I continue to work on the thesis, all the citations and references change in about the last third of the thesis. Not just the citation number, when I unformat the citations, it actually changed the original reference to another reference. It does this throughout a large portion of the thesis.

Any ideas?

What operating system, version of word and version of Endnote are you using? Are they shifting up one?

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