I have two manuscripts, each with their own Endnote library. Is the a way to merge both manuscripts preserving the links to both Endnote libraries? In other words, to merge also the two libraries.
There are multiple answers and some depend on the version of Endnote you are using.
For all versions (well all versions for the last 6 versions or more anyway) The important information is embedded in the document itself, so even if you lost both libraries, as long as you don’t have to unformat, the essential information to change styles and generate the bibliography are possible without access to the original libraries (hence the term traveling library).
Also, it is my understanding that importing one of your libraries into the other (recommend that with remove duplicates or run a duplicate search afterwards) even though it assigns new record numbers to the imported set, endnote should know and link the document citations to the them in the new library, for versions X5, X6 and X7 anyway. I haven’t extensively tested this though.
Finally, no matter what version, to merge the two papers, I suggest that you leave the two libraries as they are, unformat one or both manuscripts to the curly bracketed form, combine them and open both libraries and reformat the combined version. Endnote can happily use two or more libraries to do so. Then you could combine the libraries as above, and continue working with one library and the fused manuscript.
Before doing all this, I recommend making backups of the individual manuscripts and compressed copies of each of the libraries incase you are unhappy with the result.
The plus of having one library rather than two or more, is that everything is in one place and finding the reference you are looking for is simplified.
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Thanks. I will give it a try and report back the results.
Dan