Hi,
You can still mange them. You can have up-to three different ePO Agent Version and more if you plan it right. The only caveat is to read the document for the new Agent Version Extension. If it says that it does support all the pass versions, then you are good to go.
1) Import the new Agent Extension.
2) Import the new Agent Key Updater.
3) Wait to see all your Agents are communicating.
4) Import and deploy the New Agent Version.
5) You can still use the old Agent version for the older systems if you need to deploy it again.
Have a great day.