Recently I had one of these head scratching moments…. We were connecting an on-premises Active Directory (approx. 80,000 objects) to Office 365 using Azure AD Connect. We had a list of OU’s that was supposed to be synchronized with Office 365 and after running the Azure AD Connect wizard all objects in the corresponding OU’s were synchronized to Office 365.
The next day we got feedback from the organization the wrong OU’s were synchronized and that we had to select different OU’s (we configured the OU’s correctly, but the list we got was not correct).
When you deselect an OU in the Synchronization Service Manager (miisclient.exe in the C:\Program Files\Microsoft Azure AD Sync\UIShell directory as shown in the following screenshot) you would expect that all objects in this OU are no longer synchronized and would disappear in Office 365.