Automatically syncing your EndNote Desktop library with EndNote Online is a great way to keep a cloud-based back-up of your library, as well as being the way to share your library (or individual library groups) with up to 100 people.
However, sometimes this syncing can go wrong, and it can be quite difficult to get it back on track. So one option is to completely erase what is in EndNote Online and reset it with a new sync of your EndNote Desktop library.
To do that, follow these steps:
Open EndNote Desktop on your computer. Make a back-up of your library by going to File –> Compressed Library, and saving the whole thing, including file attachments.
Click on Edit –> Preferences –> Sync. Untick Sync Automatically and then restart EndNote.
The trash must be empty, so if there is anything there, right-click on the Trash and choose Empty Trash.
Open EndNote Online ( http://www.myendnoteweb.com ). You will need to delete all references, trash, and groups from here.
To delete all references, first go to My References.
Then click on All My References, tick the All box and press the Delete button. If you have a large library, this will delete all the references in the library, including any not not listed on this page. (You would get a confirmation of this where you could click OK.)
Once they have all been deleted, you will need to empty the Trash. To do this, press the Empty button beside the Trash.
To delete any groups, go to the Organize tab and click on Manage My Groups.
Then press the Delete button to the right of each group, and press OK to confirm for each one in turn.
If you have shared a group, you may want to first open Manage Sharing so you can keep track of who you shared it with and be ready to re-share it when it is reinstated. Press Delete All to remove everyone, and then go back to the main screen.
Go back to All My References and check that that you have no references, trash or groups.
Back in EndNote Desktop, return to Edit –> Preferences –> Sync.
Add this to the end of your email address in the sync preferences: #!resetLocalSync
( Note! This is case-sensitive. It is not #!resetlocalsync, but #!resetLocalSync )
Click OK to close the preferences.
Then click the Sync button on the toolbar.
EndNote will 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.” Click OK.
Another message now appears: “Your local sync state has been reset. Please re-enter your E-Mail Address, restart EndNote, and sync again.” Click OK.
Close EndNote Desktop and open it again. Make sure you are in the library you want to sync with EndNote Online.
Again, go to Edit –> Preferences –> Sync. Remove the bit about local syncing from the end of your email address. Ensure you just have your normal email there now (and password), and tick the box to Sync Automatically. Click OK.
Click the Sync button on the toolbar. You will once again 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.
You will be prompted to make a backup. If you have not done so already, you should create a compressed back-up copy of your library. If you already have done so, you can click No.
A complete, new sync will then begin, using your EndNote Desktop library as the source. Note that, depending on the size of your library and number of PDFs, this may take some time.
When it finishes, return to EndNote Online and confirm your library is copied there.