I received a Word 2013 document back from an editor that was originally created with Endnote 7 and using Track changes. The changes were accepted and new comments made. When I try to add a reference (as requested), it no longer recognized the previous endnote citations and simply creates a new list below the previous reference list and adds my new citation as  and not numbered accordingly among the prior pre-existing references.
Is there any way to re-recognize the previous references?
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.
Alternatively, I would try to convert your endnote citations to unformatted citations in the original document (after accepting the tracked changes) and then compare that document to the document you received back from the editor (after accepting their tracked changes, and who did obviously remove all fields) - Then you need to go thru and accept the changes the editor made, but not accept any of the citations.
Probably less tedious than reinserting all the citations.
What I did and worked for those word files that had more number of references recognized in my EndNote is as follow
In your word document, go to EndNote tap and click on “Update Citations and Bibliography”. This action will show the number of recognized references in your EndNote library which is apparently fewer.
In your word document, go to EndNote tap and click on "Export to EndNote
Select “Export Traveling Library”
Choose “An existing EndNote library” and click OK
Done! Now you have the remaining references in your EndNote.
Hope it works for you!
The day is started using EndNote, my writing became like a curse to me. It created difficulties in every step: from installing to writing my manuscript. They have the worst kind of customer service. I don’t understand how this kind of company exist in scientific community. This thing is not a citation manger. It’s more like a citation ***edit***er. Now, it’s 11.07 PM and I am just pissed of with this ***edit***ing software for last 24 hours this time. This is a pain! This is really a pain. The latest thing it did: it don’t recognise already inserted citation. It just creates a number which is already existed and then mess it up while updating citation! ***edit***er! I know, you will be continue to make money out of this ***edit*** software and researchers will continue suffering!
It can be a very powerful and adaptive software, but that means you should watch some webinars or take some courses and learn how to use it effectively. This is true for any referencing software. Sorry for your struggles.
here are some resources from their company.