Hi Argacia2013,
Some years have passed since you did this, though I am doing the same thing now. However when I go to edit - preferences - sync - and change the details to my second endnote web account - then hit sync the prompt 'this library is different to your last sync, do you want to merge libraries ’ still comes up. When you changed your details and then hit sync did this also happen to you?
Do others have problems syncing seperate libraries to seperate online accounts? To make clear I have two online accounts in an attempt to get around the problem of not being able to sync two libraies to one account. Cheers!