PDFs deleted when transferring from Endnote Web to PC

I have discovered (the hard way!) that transferring references from Endnote Web to a PC library deletes existing PDFs from the .data folder. This happens whether or not you tick the ‘Allow duplicates’ box on the Transfer pop-up window.

On the Endnote Support & Services webpage there is a notification about ‘Transferring file attachments between Endnote and Endnote Web’  which says that you lose the link and the file must be reattached (http://www.endnote.com/support/enwfaqs/Import/faq17.asp). I don’t think it’s clear that these FILES are DELETED. I don’t keep additional copies of the PDFs elsewhere (network space is at a premium), so now I have to go and try to find all the original PDFs and re-link them again.

There’s nothing about this on the Endnote Help pages and there appears to be no way to prevent the references in the PC library from being overwritten. During a test today duplicate references were not created whichever ‘duplicate’ option I chose, whereas yesterday they were.

I’m using Endnote X.0.2 (is that Endnote X1?) and Windows XP. Have I missed something, obvious or otherwise? Do I just have to make sure I  backup the .data every time?


Hello Sue,

If the references in your web library were transferred from X.0.2 before attachments were added, and are subsequently transferred back to your X.0.2 library, you are replacing the X.0.2 version with the web version without the attachments. The transfer process is replacing sets of references from the source to the destination. Duplicate checking is not involved.

Can you confirm if the records in your web library have file attachment URLs. Does transferring from the desktop to the web library update the field with a non-editable link? Does transferring back down from the web to the desktop library keep the link intact? That is how it is currently designed to work so that file attachments are not lost.

If that is not what you are seeing, please contact Technical Support. I also want to mention that FAQ 17 has been updated to reflect current design as described above.

-          Mathilda, the EndNote team

I should clarify that duplicate detection can be used when transfering records from your web library to your X.0.2 library but not in the other direction. Sorry for any confusion.

  • Mathilda

The PDFs were attached before any transferring happened. I’ve been using the option '“Copy this file to the default PDF folder and create a relative link.” Yes, the Web versions have non-editable links for the PDFs.

I’ve been doing some experimenting using direct and relative links for the PDFs. The direct ones continue to work after transfer where the relative links (which make a copy of the PDF) don’t. The copies of the PDFs that were created in the library.data/PDF folder are deleted when you transfer from the Web to the PC. Checking or not checking the ‘Allow duplicates’ box doesn’t seem to have any effect - duplicate references in the PC have their PDF copies deleted. Non-duplicate references are not affected.

A workaround would appear to be simply to not use relative links for PDFs. Unfortunately that means redoing all the links in my libraries. Maybe the problem is with the ‘Allow duplicates’ option? Shouldn’t it not transfer references that are already in the PC library?


This sounds like an issue that was resolved in a later release. Please look for a separate correspondence from me with details on an upgrade.


I managed to get an upgrade to X3 which has solved the problem of the PDF files being deleted. However, I still don’t understand why the ‘Allow duplicates’ checkbox doesn’t seem to have any effect on which references get transferred.


For Transfer, EndNote tracks matching references. From EndNote’s Help, “A matching reference is a reference that was entered once and then was transferred from EndNote Web to desktop or from EndNote desktop to EndNote Web. If you entered the same reference twice, once in EndNote Web, and then again in EndNote desktop, the records will be flagged with different Reference numbers and will be considered duplicates rather than exact matches.”

So Allow Duplicates only applies when transferring “new” references from your web library to your desktop library.

Hopefully this clarifies the behavior but if not, please post again.

 - Mathilda, the EndNote team