culling orphaned pdfs from EN

When you delete a pdf from Endnote (by clicking the delete key while the pdf is selected in the attachements field) the pdf does indeed disappear from the EN database, but the pdf remains. I just discovered this–I have dozens of orphaned pdfs, some of them huge, sitting around on my harddrive. Is there a way to figure out which are valid and which are not?


If this is true, and I haven’t tested it, I would suggest copying the library to a new location, checking whether that  doesn’t copy one or two of the known orphans and then deleting the original. Which version of Endnote are you using?  

It’s definitely true. Using mac 6.0.2. I’m not sure how copying the library to a new location would clean things up–the pdfs are in the library folder.


Copying it with endnote (copy library) - or compress library.  I expect it will only included linked files.  

I’m in the midst of a project so am leery of such a big operation. Is it safe, in your experience? Does EN rewrite the enclosing folders of attachments when it does this? I’ve got two varies of enclosing folders: those with a series of numbers, and another sort with the name of the pdf incorporated. I’m guessing that the numbers are the most recent style.


If your computer has the memory, what is the risk.  Don’t delete the other version?   --and keep a compressed version?  How big is your library?  I know you can compress a part of the library.  The record number retention isn’t as important as it used to be, so you can also move them to a new library, but you will lose any “groups”. 

I suspect your original question to tech support might yield a better solution from their end.  

My library is pretty huge (around 30 gigs) so a copy operation is not something I’d want to do just for a test! I’ll get in touch with support about this. Thanks.

Mortimer, do you have any updates with this issue? I have your same exact issue and I’m using EndNote X6 (patched to 6.0.2) for Macs.

No, no updates–I’ve been too busy to pursue it. But it’s come up at least a dozen times since then, and I’ve got orphaned pdfs sitting on my drive. I’ll enter a ticket today to see if it goes anywhere.

Just got this answer:

Thank you for contacting Thomson Reuters Technical Support.

I am sorry to hear that you are facing this issue with EndNote and I am happy to assist you.

I was able to replicate this issue by deleting a PDF from a reference in a library. 

Currently, there seems to be a known issue that attached PDF file is not being removed from the .DATA folder after deleting the reference from the library or the PDF from the reference. We had reports from few users about this issue. We apologize for any inconvenience this may cause.

This issue has been already reported to our development team and they are working on this issue. However I could not assure you the time frame on when they could find the possible resolution. However I can assure you that our developers will look into all the possible causes of this issue. I will contact you in case they need further information. 

We appreciate your effort to bring this to our notice. At this time, only workaround would be to open the PDF folder within the .Data folder and remove the old PDF file. 

I will go ahead and close this case for now, however if you have any questions it can be easily reopened at any time by a reply. In the meantime, we appreciate your patience and understanding while we continue our research on this issue. 


Thank you for posting their response. 

When I contacted the Support team, they told me to do a recovery on the library and that should fix my issue. Guess what? That didn’t fix the issue AT ALL! Anyhow, here’s waiting for patch 6.0.3!

By the way, I hope that whenever a patch comes out for the Mac version to fix this problem, it also comes out with a method to determine which PDFs in the Data folder are orphans (i.e., no longer linked to any reference) and can be removed. I’m sure I have a lot of orphan PDFs taking up unnecssary space. I didn’t discover this issue until recently.

This is apparently a Mac-specific glitch, which is still unresolved in the current release for OS X: EN X7.0.1 (Bld 9257). The pdf-attachment stays in the DATA folder, even when the entire corresponding reference is deleted from the library. Moreover, the subfolder where the attached pdf is stored, is named only by an uninformative numerical identifier, which makes it hard to find any orphaned pdf even manually (as suggested by the TR Support).

I’ve just checked my previous EN X4.0.2 (Bld 7031) under OS X 10.8.5 (Mountain Lion), and there this function works properly. Furthermore, the subfolder to DATA, where the attached pdf is stored, is named by the pdf name, plus a numerical identifier (e.g., the attached pdf “Berman et al 2008.pdf” is automatically stored by EN as: “Libraryname.Data/PDF/Berman et al 2008-2165291264/Berman et al 2008.pdf “). When the attached pdf is deleted from the reference, both the pdf and its subfolder are also deleted.

Does anyone have any update on this? I’m in the situation where I know I have orphaned PDFs which are taking up disk space, but I have no way of automatically finding them. Seems to me there is no rush to fix this issue. Running on Mac OS X.


  • Pete

I can only say that it has still not been fixed…

Anyone has any news?

.I am on X7 (build 9013).

It’s now over 4 years since my previous post on this subject. Is this feature still not available? Seems pretty basic to me!


  • Pete