Just checking - did you follow the manual’s instructions (below)? And after converting the Word citations to EndNote, did you replace the original Word citations in the document with the EndNote citations? It sounds like you’re maintaining both types within the document but the Word citations should be replaced with the EndNote references.
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Converting Word 2007 and 2010 Citations to EndNote (pp. 175-176 or search using Help)
Word 2007and 2010 includes a Reference tab, where you can use commands to insert Microsoft Word
footnote or endnote citations. These footnote and endnote citations are not used directly by EndNote’s Cite
While You Write feature (although you can insert an EndNote citation within a Word footnote). If you have
citations already entered into Word, you can copy the reference information into an EndNote library and then
convert the Word citations into EndNote Cite While You Write citations.
Note: The Word citation conversion features requires that your computer have the Microsoft .Net Framework installed.
To export Word 2007 and 2010 citations to an EndNote library:
1. Open the Word document that contains the citations.
2. On the EndNote tab, in the Tools group, select
Export to EndNote and then Export Word 2007 Citations.
To export the Word 2007 and 2010 master citation list to an EndNote library:
1. Open the Word document that contains the citations.
2. On the EndNote tab, in the Tools group, select
Export to EndNote and then Export Word 2007 Master List.
To convert Word 2007 and 2010 citations to EndNote citations within the document:
1. Open the Word document that contains the citations.
2. On the EndNote tab, in the Bibliography group, select
Convert Citations and Bibliography and then Convert Word 2007 Citations to EndNote.
.