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So, I just did a rebuild of my server and a fresh WHS 2011 install. I pulled all of the pooled drives, installed WHS on the system drive, and then turned the system off before reconnecting the pool drives all back up and restarting. Now the pool is fine, it sees all of the drives and recreated the pool just as it was before the re-install with all of the data on it, woo hoo!
WHS is less happy though, it can only see the (empty) default shared folders created during the install and not the real shared folders in the pool. So, how do I point it to the 'other' default folders as well as all of the additional shared folders in the pool?