If the references are correct in your EndNote Online account:

www.myendnoteweb.com: DO NOT follow these steps.

Instead, simply make a new, blank EndNote desktop library and sync to that.
Remember: DO NOT save an active library to iCloud, OneDrive, Dropbox, etc.

"Resetting" Sync:

There are many cases where the user just needs to “start fresh” with sync, usually because they didn’t realize that after syncing, deleting on one side will cause information on the other side to delete, or because they didn’t understand the workflow and wound up with a large number of duplicates.

  1. Do a backup of the original library that contains everything that you want.
  1. Disable automatic syncing in EndNote Edit menu, (EndNote menu on the Mac), Preferences, Sync and also remove your e-mail address, click Apply > OK and restart EndNote.
  2. Delete all references and all groups from EndNote Online, with the exception of Shared Groups and ResearcherID Groups.
  3. Online
  4. Empty the Trash both in the EndNote Online application AND in EndNote desktop.
  5. In EndNote desktop, re-enter your e-mail and add this to the end of the address in the Sync preferences: 
  6. #!resetLocalSync
    Note that this is case sensitive -- #!resetLocalSync type exactly as shown or copy paste.
  7. For example, if the email address was MyName@crandon.com.au
  8. we would change this to MyName@crandon.com.au#!resetLocalSync
  9. Click Apply, close the preferences.
  10. Reset
  11. Click Sync. icon or Tools > Sync.
  12. EndNote will then appear to authenticate and return the prompt:
  13. “A Sync library can be linked to only one account. Do not proceed unless you intend to break the link to the original account.” ( Note if you are not using the original library then the warning message may appear: " You are about to sync a library that is different then the last..." : Click YES )
  14. This happens because we tricked EndNote into thinking it authenticated against another user.
  15. Click OK, and EndNote will purge any knowledge of a previous sync.
  16. 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.”
  17. Restart EndNote.
  18. Open the Sync Preferences, enter the correct e-mail and password in the sync settings.
  19. Continuing with the example used above, I would now re-enter MyName@crandon.com.au 
  20. as my email address in the Preferences.
  21. When you next click Sync, you will once more get:
  22. “A Sync library can be linked to only one account. Do not proceed unless you intend to break the link to the original account.
  23. Click OK.
  24. You will also be prompted to make a backup. This is up to you, but of course we recommend it.
  25. A complete sync will then begin.

A few important notes about this procedure:

• The above steps essentially cause a first-time sync, so it could take some time to complete, especially if the library is large or contains a large number of file attachments
• This process is ONLY for users who need to “start over” with Sync. 
• To perform these steps, you need to have a correct version of the library available to sync from. If you do not have one, you will have to clean up existing file or create a new library with exactly the information you wish before beginning the steps above.
• Following these steps will solve the issue even if there are multiple desktops and iPads syncing to this account. The deletion of the original material on the Web will cause all of them to be cleared and after the last step, all of them will be repopulated upon their next sync. Note, if the iPad or another client attempts to sync while the new sync is in process, it may retrieve incomplete data. This should not be a concern as once the original library’s sync is completed, syncing from the other clients will bring in the rest of the information.