I have discovered that even after I have deleted certain PDFs from a reference in EndNote library, the actual PDF remains in EndNote’s PDF library. How can we have the PDF automatically deleted when the PDF is deleted from the reference?
I’m running EndNote X6.0.1 on Windows 7 Pro and deleted pdfs are removed from the PDF folder.
Did you upgrade X6 with the latest patch? See http://endnote.com/downloads/available-updates
Also, you say “certain pdfs” so does this mean the problem occurs inconsistently? If so, are you able to discern a pattern?
If you’re experiencing problems after updating your software pls. describe how you’re deleting the pdf as it may highlight another issue.
This thread reports a similar “feature”, but I can not duplicate it with the Windows version of X6.0.1.
Hmm…it doesn’t do it on mine. Of course, my EndNote has been in existence since oh, I think EndNote 6 or something like that and have been ugraded through the years and now is at X6. I have the Mac version.
Are they file attachments or a “figure” attachment (which I didn’t test)?
I have been using endnote since, it didn’t have a number?! … but I tried the deletion on a small library specifically built to test the phenomenon. I openned the record and clicked on the pdf and hit the delete button. How are you doing it? then where did you look? Are they in the .DATA/pdg folder in a folder?
What happens if you save as to a new library name? or compress, the library and open it in a new place?
These are all PDFs. I have the option where the file attachment is copied to the default PDF folder and a relative link is created. I can delete a PDF from the refernence window, no problem. The PDF icon disappears. However, if I go to the folder where all PDFs for EndNote are stored, in my case “Library Database.Data”/PDF , I can locate the PDF that was deleted from the reference but remains within that default PDF folder.
In fact, I tested this also by the following steps:
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Create a new library with one reference.
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Drag and drop a PDF to that reference.
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Double-click PDF icon in reference windo to open PDF.
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Close opened PDF
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Navigate back to reference window, select PDF icon and hit “delete” on keyboard. PDF icon disappears as expected. I hit “save”. Then I quit EndNote completely.
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Now, on the computer I navigate to the EndNote library PDF folder for this new library and lo and behold that PDF file is still there even though it no longer exists in EndNote library itself.
I’ve been using EndNote when it was first owned by Niles software, whatever version number that was! 
Sounds like a Mac issue. It must be a bug and hopefully they are watching this thread!??
What happens if you save as to a new library name? or compress, the library and open it in a new place? does that get rid of the offending “deleted” PDFs?
Just following up on a prior question but did you upgrade your X6 software with the patch (for Mac)? See: http://endnote.com/downloads/available-updates
If you’ve installed the patch and are experiencing problems contact tech support as it might be a Mac issue as Leanne noted :http://endnote.com/contact/customer-support
I’ve followed the solution that Support gave, which was to do first a recovery on the library, and if that doesn’t work, an Advance Recovery. Well, EndNote X6 (with the patch), kept crashing in the midst of doing a recovery so I opened up EndNote X5 to do the advance recovery. After that, I opened it with EndNote X6 and proceeded to check to see if PDFs get automatically deleted from the PDF data library. Guess what? It doesn’t work. PDFs still don’t get deleted from the appropriate folder.
Indeed, this finally has been acknowledged by EndNote Supportt to be a Mac issue. Check out the response they have to Mortimer:
http://community.thomsonreuters.com/t5/EndNote-General/culling-orphaned-pdfs-from-EN/td-p/38489