Online P2V conversions in System Center Virtual Machine Manager are based on point-in-time snapshots. Therefore, it’s no wonder, you’d receive following warning when you try to Online P2V a Domain Controller:
The simple reason for warning message in SCVMM is you may receive following error on a virtual Domain Controller when you boot it after you previously P2V’d it online: “The Active Directory is rebuilding indices. Please wait…” The integrity of the database is now at risk. I think we can safely assume the warning in the P2V Wizard in System Center Virtual Machine Manager isn’t an invitation to a game of ‘chicken’… The same error can be expected when you use the Disk2VHD utility. There’re four steps to perform a good P2V conversion of a Domain Controller. These four steps’re additional steps to perform with usual best practices when performing P2V conversions.
Full Article: AD blog