I have an ePO with about 2500 and would like to integrate it with Active Directory to have a better controll of the machines that get added to AD, and the machines that are now on AD without Antivirus.
I wonder what will happen to all the containers that i have if i choose to sync now with AD.
When you configure an Active Directory sync, you can choose whether or not to move systems that are already in ePO to the containers as defined by AD OU, or leave them where they currently are. Systems that are added via AD sync that were not in ePO previously will show as unmanaged until you get a McAfee Agent installed on them.
A bit of advice, unless you have an extremely well-managed AD, it is categorically better to only bring over the objects and not the hierarchy. Especially if ownership of your AD is not the same as your ePO.