I have just ran into this problem about 10 minutes ago. I've done some research and I've managed to fix it. The outcome of this error, is that it forgets all your sources and doesn't know what packages you have installed. If you try to add a new source while its in this state, it adds it, then gives you the error again, and you still have no sources or packages. Now the fix to this, is to use iFile, or if you just have openssh that works too, and you want to navigate to / > var > lib > apt > lists, and delete everything, EXCEPT!!! the partial folder. Once you're done deleting them, open Cydia, and the error message should be gone. Now you will notice, that still you have no packages or sources in Cyida. The next step to fix this is to simply add a source, wait for the contents to download, and when you hit return to Cydia, everything is back again. Hope this helps.
