I think now it's official: The EMC-Error is caused by duplicated SIDs... :(
The way I recoverd my Exchange-VM:
- Shutdown Exchange-Services
- Copy the entire Database-Folder to a temporary location (or use the virtual data-disk for the new VM)
- Shutdown Exchange-VM
- Install new VM or import a template and change the SID with sysprep (!!)
- Remove old server account from AD
- Rename the new VM with the old name and join the domain
- Add the server account to the AD-group "Microsoft Exchange System Objects/Exchange Install Domain Servers" (to avoid MSEXCHANGEADTOPOLOGY-server startup error)
- Copy the Exchange-database to the same driver/folder
- Run "Setup /m:RecoverServer /InstallWindowsComponents" from Exchange 2010 SP1 Folder