From the EMC2 archives,
"Now limit override is NOT soft limit override. There is no such animal. Limit override means let me move the offending axis off from the real limit switch it has hit. This can happen any time you have real limit switches hooked up properly and you are jogging the machine around before you home it."
I would temporarily comment out the 'soft' limits in the ini file and start up the machine to move back into safe limits, then close down and restore my old ini values.
I would also consider changing my 'soft' limits to + the axis travel, and add hard limits. If you were running servos with encoder feedback, I would also consider (if possible) manually moving the 'bad' axis back into limits. You mentioned "Stepconf," are you using steppers with encoders?
I don't believe there's any encoders there... I'm guessing that EMC just assumes that it moved whatever pulses it sent to it.
sometimes what I end up doing is just turning off the machine, seeking way out,
turning back on the machine, seeking back to "home" and then zeroing it out.