Answered By: Rudy R. Barreras
Last Updated: Jun 14, 2023     Views: 9285

Occasionally EndNote Desktop and EndNote Online will not Sync correctly or, you may wish to Sync a different library from the one you are currently Syncing.

Before attempting the procedure below ensure that your EndNote Desktop library is backed up in a Compressed Library.

  1. Open EndNote >click on Edit>Preferences>Sync. Disable all automatic syncing and then restart EndNote.
  2. Make sure the Trash is empty both in EndNote online as well as in EndNote desktop. For EndNote online, Log into your EndNote online account http://my.endnote.com/. Delete all references and all groups from EndNote online, with the exception of any Shared Groups or ResearcherID Groups that they may have. To do so, login to EndNote online and check the reference under All References group and click on Delete. You will need to delete the groups as well, because when they sync with EndNote desktop, the groups will sync with the desktop. To delete the groups, go to the organise tab and click on Manage My Groups. Select the groups and delete.
  3. In EndNote desktop, open the correct copy (backup copy) of the library. Open EndNote>Edit>Preferences>Sync. Add this to the end of your E-Mail Address in the sync preferences: 
    #!resetLocalSync
    Note! This is Case Sensitive -- resetLocalSync not “resetlocalsync". 
  4. Click OK to close the preferences, and then click the Sync button.
  5. 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 EndNote is checking authentication. Click OK, and EndNote will purge any knowledge of a previous sync.
  6. EndNote will then display the message, “Your local sync state has been reset. Please re-enter your E-Mail Address, restart EndNote, and sync again.” Click Ok.
  7. Close EndNote and open it again. Close all libraries then open the library which you'd like to sync with EndNote online.
  8. Again go to your sync preferences; enter your username/password and setup automatic sync settings. 
  9. When you next click Sync, you will once again 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.
  10. You will be prompted to make a backup. While this step is not required, it never hurts, follow the onscreen prompts to backup.
  11. A complete sync will then begin. 

Note! The first full sync can take a significant amount of time. Time taken to sync depends upon the size of the PDF attachments and number of references in the library.

Once the sync is complete, login to your EndNote online (http://my.endnote.com ) account and check whether you have the same set of references.

Now go to your desktop computer and create a new library and sync again. This will bring all the references from the EndNote Online library to the EndNote Desktop library. To do this,

  1. Open EndNote.
  2. Click on File > New > Choose the destination to save this library > Save.
  3. Click on Tools > Sync.

Note! Do not sync with the existing library as it will merge libraries and create duplicate references. The time taken to sync depends upon the size of the PDF attachments and number of references in the library.

For more information about syncing please refer to the EndNote Knowledgebase : https://support.clarivate.com/Endnote/s/?language=en_US

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