Extremely slow progress

Depends on your version of Endntoe, but If moving large blocks of text with citations, you probably want to turn off CWYW and also turn off the hyperlinking of citations to the bibliography (in format bibliography).  You many even want to unformat the citations to their temporary form.  This prevents any inadvertant corruption of the rather large hidden fields that hold the endnote information.  

So – Unformat to temporary citations from the toolbar or ribbon (NOT remove field codes, or make plain text) 

This should also turn off CWYW.  But if you go into Format Bibliography> and untick the box on the first tab, “link in-text citations to references in the bibliography”  

Later you can manually format from the format bibliography menu, turn back on CWYW and even turn back on the hyperlinking if it is something you would like active in your document.