Occasionally EndNote Desktop and EndNote Web will not Sync correctly or, you may wish to Sync a different library from the one you are currently syncing as EndNote Web can only sync with one EndNote Desktop library.
These notes cover two scenarios: EndNote Desktop is correct but EndNote Web is not, or you want to sync a new Desktop library. While the instructions are straightforward, follow them carefully to ensure you don’t damage your library.
Before attempting the procedure below make sure that your EndNote Desktop library is backed up in a Compressed Library.
1. Open EndNote Desktop > click on Edit > Preferences > Sync. Disable automatic syncing and then restart EndNote i.e. if the Sync Automatically check box is ticked, untick it. Click OK. Restart EndNote
2. Login to EndNote Web, then delete all references from EndNote Web. To delete the references, check the box marked All under the "All My References" heading and click on Delete. This will delete all references, not just those on the page you are viewing.
3. Delete any groups that you have with the exception of Shared Groups and ResearcherID Groups. To delete the groups, go to the "Organise" tab and click on Manage My Groups. Select the groups and click on delete.
4. Empty the Trash in both EndNote Web AND in EndNote desktop.
5. In EndNote desktop, add this to the end of your E-Mail Address in the Sync preferences: #!resetLocalSync - note that this is case sensitive --
#!resetLocalSync NOT #!resetlocalsync.
For example, if the email address was firstname.lastname@example.org, you would change this to email@example.com#!resetLocalSync
6. Click OK to close the preferences, and then click the Sync button (the circle with arrows on the top menu bar).
7. 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 have tricked EndNote into thinking it authenticated against another user. Click OK, and EndNote will purge any knowledge of a previous sync. 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.
8. Restart EndNote.
9. Open the library which you'd like to sync with EndNote Web
10. Open the Sync Preferences, reset your correct username/password and click the automatic sync checkbox.
11. When you next click Sync, you will once more 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.
12. You will be prompted to make a backup, which is recommended. However, if you are confident you already have a backup then you can skip this step.
13. 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 the number of references in the library.
14. Once the sync is complete, login to your EndNote Web (http://my.endnote.com) account and check whether you have the same set of references.