I found this article that shows step-by-step how to re-create the directories in IIS. Article
So I created the backup of the site by following Step 1, followed the rest of the steps, waited 15 minutes. Rebooted the computer. Waited 15 minutes. Rebooted again. The directories never came back. I looked everywhere on the net for ways of recovering from the configuration file I had created in Step1. They all talk about restoring from within IIS from backup points. I tried going back to the first backup point after installing Exchange 2003, but no-go.
Now I was looking at re-installing Exchange just to get OWA back. I came across a part of a post about moving IIS websites:
- If you have another IIS6.0 machine you can right click on the Default Web Site and select 'save configuration to file...' and then take the XML file it produces, copy it to this machine, right click on the 'Web Sites' folder and select New and then 'Website (form file)...". Point it to the XML file, select read and e that - it will create a duplicate of the Default Web Site from the other machine.
Just goes to show how important that backup is before you start to work, but more so....knowing how to restore from it.