Upgrading your organization from current versions to Exchange Server SE

KevinJ1230 Deleting the server from VMware, I guess removed the VM itself. That's kind of like reformatting the machine where Exchange was installed. Indeed, when CleanupActiveDirectoryEMT.ps1 is run, that will remove the Exchange server object itself from AD from under Exchange organization. This is the server object that we check for prerequisite checks during Setup. So, this needs to be gone before Exchange SE CU1. Running the script will remove various Exchange related things from AD, not the AAD/Entra Sync, no. Please check the documentation that tells you how to prepare for running it. Sounds like you already did everything before except running it. Note (as per the updates section) that you might need to run it again if you update your tools to Exchange SE RTM and then Exchange SE CU1.