You will sort this out, i can't see how by doing what you did , that you done any 'damage' to your second drive. You say that you changed the jumper settings ,why? They had to be set as slave before you did anything, what are they set to now? Go back and check that the jumpers are set for slave on your second drive, and that the cable is inserted correctly . Like i say by doing what you done there should be no problem, its just a 'glitchy' thing.
Hope this helps