Understanding hybrid Azure AD join and co-management

Thanks for the valuable article,

We are currently using Configuration Manager and looking into using Intune co-management. But when we installed Office, users have selected the option to "allow organization to manage my device" so we accidently ended up with thousands of devices registered in Intune (those are domain joined devices currently managed by Configuration Manager). Now when we want to enable co-management, we are looking for the proper way to cleanup Intune from those accidently registered devices, so we can enable Azure AD sync to bring on-premise domain devices into Intune properly and then enable co-management. What is the proper way to do? can we just delete those devices from Intune? we can't ask thousands of users to disconnect work/school account and I couldn't find a way to do that administratively on many computers? Thanks