Maura Daffern,
Were you able to fix your corrupt site?
We just experienced a similar issue copying an OD site (dev, fortunately) using AGO Assistant. Copy seemed to work fine, but after deleting the copy, the original no longer would recognized any of our open data groups in the Groups Manager, and wouldn't show any data in the site. Unfortunately, I can't say for sure whether or not the original OD site worked after copying, but before deleting the copy.
Thanks,
Dan