I recently put Azure AD Sync in place for a client that was previously syncing IDs to Office 365 using the Windows Server Essentials Experience plugin on a DC running Server 2012 R2. This was very easy to set up and simple to reconcile the existing on prem AD users to the accounts they had been using already on Office 365.
From what I understand the Essentials plugin uses a variation on DirSync to synchronize your local users to Office 365. I read that DirSync would eventually no longer be supported soon. With this in mind I prepared to upgrade the sync to use the newer Azure AD Sync tool. The install and initial config for the on prem DC was easy but after my initial sync I noticed that only my on prem account had reconciled with its Azure AD counterpart. All other on prem accounts ended up getting cloned, resulting in two accounts for each user: their original Azure AD account and another new account using the default @onmicrosoft.com username. Of course, their on prem AD account maps to the @onmicrosoft account and not their original Azure AD account as I would have hoped.
Now I am left with a bit of a mess on my hands and unsure how to proceed. I would like to reconcile the other accounts to the Azure AD accounts they currently use but i have not seen a way to cleanly do it. The only method I can think of is to back up each user's data from 365, delete that account then transfer the license to the @onmicrosoft account and set up their stuff again. It would be a painful process for each user and one I would rather avoid.
Has anyone else run into this? If I were starting with a clean Azure AD, this would have been a very simple process but none of the scenarios I have read about gave me an idea how to set this up between an on prem AD with an already populated Azure AD let alone reconcile after the fact.