Trouble Syncing Endnote X6 with EndNote Web

About a month ago, my group’s EndNote X6 desktop databases was synced with our EndNote Web platform, which resulted in duplicating or even triplicating most of the references. I managed to delete, en mass, all of the duplicate references in the desktop version. After spending quite a while on the phone with customer support, I was told these changes would be reflected in the Web version, once a sync was performed. When I attempted to sync the two platforms, none of the changes were reflected in End Note web, so this data base has over 10,000 references which is very unmanageable. For comparison sake, the desktop version only has 5000. When trying to manually delete the duplicates in this library, none were identified, because there are slight variations (thus negligible variations) in many of the  references, so the " Find Duplicates" feature does not work in this platform, according to customer service.  So, the three main issues I am having is…

How to delete the duplicates in EndNote Web? 

How to ensure that this duplication process will not happen again?

How to ensure that any changes made in one of the platforms will be reflected in the other, seeing that many changes being made in one platform are not being seen in the other?

Any help will be greatly appreciated