EndNote - How to reset sync

Sometimes, syncing your online and desktop EndNote library causes the references to duplicate. If this is happening, you might need to reset the sync. Here's how:

NOTE: The reset sync process will delete the references from the EndNote online account and initiate a fresh sync from the desktop library. Please note that once the references are deleted from the EndNote online account, it is not possible to get them back. Therefore, first check if you have the correct set of references in EndNote desktop library.

Create a backup copy of your library before proceeding with the reset process. To save a backup, please go to File > Save a Copy, and save the library.

Now delete all the references and groups (except ResearcherID groups) from your EndNote online account. Please see the below links for instructions:


Now do the following:

1. Open your preferred library in EndNote X8, click on the “Edit” menu and select “Preferences”. Uncheck “Sync Automatically”. Restart EndNote. Do this on your laptop also.

2. Empty Trash on both your desktop library and online library

3. Now go to “Edit” menu > “Preferences”, click on “Sync” and add the following to your E-mail address under EndNote Web Account Credentials: #!resetLocalSync This should then read as: [email protected]#!resetLocalSync

4. Click “Save” and close the “Preferences” screen.

5. Click on the “Tools” menu and select “Sync”.

6. EndNote will then appear to authenticate and return the prompt: “A Sync library can be linked to only one account. Do not proceed unless you intend to break the link to the original account.” This happens because we tricked EndNote into thinking it authenticated against another user. Click OK, and EndNote will purge any knowledge of a previous sync.

NOTE: If you didn’t get the above message, please close your library from “File” > “Close” Library and create a new blank library from “File” > “New” and Save it in your Desktop. Once it is done, go to “Tools” > “Sync”. This will bring up the above message. You can then open your library and go to “Tools” > “Sync” again and follow the steps below.

7. EndNote will then display a message, “Your local sync state has been reset. Please re-enter your E-Mail Address, restart EndNote, and Sync again.”

8. Restart EndNote and open the copy of your library that has the full set of references.

9. Go back to “Edit” menu > Preferences and go to Sync.

10. Enter the correct email address/password in and set up the automatic sync settings to meet your needs. The E-mail address should be reset back to your actual email address, without the added part.

11. Save and Close the Preferences.

12. When you click Sync again, you will once more get the message “A Sync library can be linked to only one account. Do not proceed unless you intend to break the link to the original account.” Click OK.

13. You will be prompted to make a backup of your library. You can create another backup of your library at this point.

14. A complete Sync will then begin.

This should transfer all the references from EndNote Desktop to EndNote online and the changes should be automatically synced thereafter.

To know more about sync, please refer to the following Knowledgebase article: http://endnote.com/kb/122170