Nothing.Might seem to be a stupid question, but what happens if I accidently would clear CMOS when the computer is up and running?
It is possible the real time clock would cease functioning while you had the jump in the clear position, resulting in the software hard crashing. However, it would do no harm to anything, and normal function would resume when you put the jumper in the correct position.
ps: I once installed a 486 90 degrees off angle. Now that let the magic pixies* out!