I think I've run into an issue with a Discoverer refresh and any search I run is fruitless. A Discoverer admin refreshed one of our business areas and apparently it deleted some of the folders. He told me he wasn't paying too close attention to the "impact" window so he doesn't know for sure if this is what happened. As the workbooks we're being reported about worked a day or two before the refresh and now they don't due to missing folders, this is the only thing I can think of what happened. The actual database tables weren't deleted as I was able to recreate the folders in the business area. However, the recreated joins still don't seem to be picked up the user tool.
We use admin tool version 10.1.2.48.18 on database 10.2.0.5.0.