Win98 won’t boot from startup disk

I swapped hard drives (master to slave and vice versa) on a Win98 machine. Though the computer recognized the swap, suddenly the files in Windows 98 (Himem.sys, and a few others got corrupted. The machine will not boot up from the emergency disk at all, will not allow me to run setup to correct the problem. What should I do? I don’t have a problem with reformatting the drive if that is what I have to do.