First of all, EndNote online can only sync with one desktop EndNote library. So please check that you are trying to sync with the correct library.
You can do this by going to EndNote (desktop) and clicking on 'Edit' then 'Preferences'. You can check which library you are syncing with on this screen, it usually has a location in your H drive.
Please note: We recommend only having one desktop EndNote library to avoid duplication and problems with Cite While you Write in Word.
If this is correct and you only have one library, then you might want to check that your online email address and password match your university desktop details? Again you can check and change this information by changing your sync preferences as shown above.
We hope this helps but if you have any other sync issues please submit your question via Library Help and we will investigate.