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I ran a stsadm -o enumsites and received 2 error messages in the output. It generates the error: The system cannot find the path specified. (Exception from HRESULT: 0x80070003). I know the URL of one of the site collections from doing some web part testing.

I cannot trace down the other site collection. enumallwebs shows nothing for the one collection I know of. The sites do not show up as orphaned.

I'm at a loss as to how to identify these sites and remove them from the configuration database I presume.

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Ok, I found out what the issue was. The site was a particularly large site restore that was deleted from the web ui in our test farm. I believe the delete timed out and left a bit of bad data hanging out in the SiteMap table.

This blog post lead me to finding where the particular site collection was located. Once I had that content database isolated, I deleted it from Central Administration and and added it back into the farm as described here. This cleaned up the corrupted sites.

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