My EndNote Sync is broken.


Sometimes you'll find that sync isn't working - EndNote might appear to sync, but it doesn't update your online library.

If your sync seems to be broken, this is the procedure you should follow:

  1. Make a backup of your EndNote Library.

    • create a compressed library, or

    • copy and paste your .enl library and associated .data folder into a safe location. 

  1. Open EndNote > click on Edit > Preferences > Sync. Disable automatic syncing and then restart EndNote. 

  1. 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, delete all references and all groups from EndNote online. 

  1. In EndNote desktop, open the copy of the library you intend to work with going forward (this doesn’t have to be the backup). Open EndNote > Edit > Preferences > Sync.

  2. Add the following text to the end of your email address in the login field: 


    Note: this is case sensitive. 

  1. Click OK to close the preferences, and then click the Sync button. 

  1. 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. 

  1. EndNote will then display a message, “Your local sync state has been reset. Please re-enter your email address, restart EndNote, and sync again.” Click OK. 

  1. Close EndNote and open it again. Close all libraries then open the library which you would like to sync with EndNote online. 

  1. Go to sync preferences, enter the correct username/password and then sync.  

  1. When you next sync, you will get “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. 

  1. You will be prompted to make a backup, you don't have to do this as you already have one. 

  1. A complete sync will then begin. 

  2. The first full sync can take a significant amount of time, especially if you have a large library. Time taken to sync depends upon the size of the PDF attachments and number of references in the library.

  3. Once the sync is complete, login to EndNote Online and check whether you have the same set of references. 


Created date: Sep 20, 2023

Date of last update: Oct 03, 2023

Related FAQs