Yes I worked with ESRI to determine what exactly was happening. It seems like previously, you would opt to upgrade to V 2.1 by clicking the upgrade site option. ESRI then chose to automate the update, however when that happened the redundant legacy site was created, which ends up being the default site that is forward facing to the public. This legacy site can't be edited. The "upgraded" site can be edited but the edits won't reflect to the public, and if you delete the legacy site you run the risk of losing everything. ESRI support staff had to manually repair this through our organizational account, but should be able to help you if the same issue is present with your site. Hope this helps!
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