The large document has around 400 citations and it is in two sections. The first half is with Mendeley and the second half is with Endnote.
Can I somehow take one of these halves and convert them Mendeley↔Endnote?
Please please don't tell me I need to do it all manually
There are instructions here on how I can import my library from mendeley into endnote. I can do that, but will this work to switch an entire document from mendeley into endnote?
-- http://canterbury.libguides.com/endnote/extra-importing
I have never done this but I know that there is a function in EndNote to convert Reference Manager citations to EndNote. If you cannot convert directly (give it a try), then convert Mendeley to Reference Manager and then import into EndNote. I am not sure whether this is very helpful but my advice is to work from the Mendeley file and see whether you can convert all of the references to EndNote before attempting to merge them.
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