C drive is know D drive

After testing a bad hard drive (disconected cd-rom drive and conecting bad hard drive to cd-rom conection to try to read the bad drive) when we rebooted like this the cpu read the bad drive as C and the good drive as D now all my files still read asbeing on the D drive and that there is no C drive. So when the machine is started you get a window with on Icons or startup. You have to go in to task manager>file>new task run and then type Explorer.exe to bring up Icons but even then if I try to run any thing it looks for it on the C drive when it is now on the D drive. Please Help