After having the exact same issue on both Endnote 7 and updated 8.2 constantly crashing on my MacBook Pro (OS Sierra 10.12.6) and being completely unworkable as I’m writing my thesis, I have discovered the following:
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- Issues arose after MPB operating system El Capitan 10.11 (I.e., if your OS is this or earlier, you should be fine) due to Apple changing their PDFkit.
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- In my Endnote Library, this has resulted in some of my pdfs being duplicated in the “PDF” folder in the .Data file of my Library. (I.e., more than one of the sub folders contained the same pdf for a given reference in my Endnote Library).
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- If you only use Endnote as a citation manager and not as a reference manager, then you can just move the “PDF” folder from the .Data folder to somewhere else. This will stabalize Endnote, but you will have to access all your pdfs manually by searching for them in the moved “PDF” folder.
Here is the fix I did (564 references, with 311 pdfs):
- SAVE A COPY OF YOUR LIBRARY!!! (put the backup in a safe place). It is easy to screw up how your library talks to the attached pdfs, so make sure you have an original untouched backup somewhere.
- Close Endnote if you have it open
- Open the .Data folder of your library, make a copy of the “PDF” folder to a temporary different location, like your desktop.
- Now create a new empty folder and name it “PDF_temporary_fixing” on your desktop.
- You now have two folders on your desktop, the copied “PDF” folder, and the “PDF_temporary_fixing”
- In this copied “PDF” folder that you have moved to your desktop, move all of the pdfs out of their sub folders and into the “PDF_temporary_fixing”. There are shortcuts that you can google on how to do this quickly instead of moving one-by-one if you have a ton of pdfs.
- Now you should have just a list of pdf files on your “PDF_temporary_fixing” folder. By doing this, you will be able to identify any duplicates of pdfs because they will have the same name (write these down). You would have a much harder time doing this if you have to go through the sub folders one-by-one.
- You can now delete the copied PDF folder, as you have now identified your duplicates.
- Go back into your .Data folder of your Library, and into your “PDF” folder that you have there, and search within that “PDF” folder for the identified pdf duplicates. Write down the folder number that the duplicates (both/all copies) are in. For example: for pdf “Smith-2016.pdf” you could have one duplicate in folder “3907727203” and another in folder “2442186214”. It is also worth it to look at each pdf in adobe to see if one has any highlights/comments that you may have made, so you know which one to keep. I also made note of which file was older/bigger to help me decide which one I would keep.
- By this step you should have a list of all your duplicates, their folders, and an idea of which ones you would like to keep.
- Now you get to go into the “PDF” folder in the .Data folder and delete the folders with duplicates!
- You’re not quite done yet, you now have to open Endnote and make sure that the references which had multiple .pdfs are still talking to the remaining .pdf in the “PDF” folder in the .Data folder. Search for each reference and click on it to see if it still opens the reference. If they all do, great! You’re done and can also delete your “PDF_temporary_fixing” folder. If not, then keep going.
- For any references that aren’t opening their pdfs, you have to re-attach them manually.
- Close Endnote
- Go into the “PDF” folder in the .Data folder, and move the folders with the references you want to attach completely out of the “PDF” folder and onto your desktop.
- Open Endnote, and search for each reference that you need to re-attach. Drag their associated pdf onto the reference in Endnote to attach manually. Do this for each reference.
- You can now delete the moved folders on your desktop, as Endnote automatically creates a new copy in the “PDF” folder.
By doing the above my Endnote significantly stabilized. I found 6 duplicated references out of 311, so hopefully this is more of a sporadic occurence. I also would recommend manually attaching pdfs to imported references instead of getting Endnote to find and attach the pdfs for you. Don’t forget to create back-ups of your library regularly if something goes wrong.
I hope this works for other people! It’s labour-intensive but salvaged my thesis, library, and prevented me from having to run Endnote in Bootcamp or Parallels Desktop.
**UPDATE #1** after one week of regular daily use, the software remains stabilized. I am curious if others have tried and had any sucess using my posted fix?
**UPDATE #2** stburrow highlights an aspect of this problem that I haven’t encountered, being the use of Smart Groups, because I have not used them in my libraries. Therefore it appears that my fix will not work if the library utilizes Smart Groups.