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I don't even know if gnome just crashed or went hidden or what.

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Try entering the following commands in terminal. gconftool-2 --recursive-unset /apps/panel && killall gnome-panel – karthick87 Mar 8 '12 at 8:34
The above commands may bring you back the panels which you have lost. – karthick87 Mar 8 '12 at 8:34
Thanks, but I ended up figuring out that if I restarted, both bars would come back for a short while, during which time I was able to simply delete the bottom bar (opening the properties dialogue to reposition it crashed things again), and then create a new one. – Owen_R Mar 8 '12 at 20:26
I'd test your recommendation, but I'm afraid I might break things even worse. – Owen_R Mar 8 '12 at 20:27

Did you use an extension to change this in gnome-shell? If so you can use the terminal to remove the offending extension from ~/.local/share/extensions/

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