1) Flatten the server/VM/whatever
2) Load the last clean backup image
3) Apply updates made since the last backup
5) Carry on ....
You do have back ups don't you?
You do develop off-line and push deployments to servers don't you?
No? Then remember to renew the notice in the front window of your house telling the potential burglars you didn't lock the place up and there all the valuable are stored.