10-17-2019 02:11 PM
I stumbled accross this threat because I am transfering my library from Papers3 to EndNote and encountered exactly the same problem as many people here, in that I ended up with lots of references und lots of seperate entries with imported pdfs that failed to match to any metadata. Like everybody here I was looking for a merge function to merge the entry with the proper metadata with the entry with the pdf, but had to learn that this function does not exist. So here is what I did instead as a workaround:
I noticed that when I imported my library as a .ris or .xml file from Papers3 to EndNote, the references had a broken link to the pdf. The workaround described in the following shows you how to fix the broken links by placing the pdfs exactly in the location where EndNote is looking for them and then using the "converting to relative links" function to move the pdfs into the EndNote library folder. You might need to play around a little to get it to work, but I hope these instructions will save you some time to get it done.
About the annotations in pdfs in Papers3: