Downstairs exhaust fan venting into upstairs?
If the downstairs fan is vented into the upstairs, replacing the fan will not do anything.  

In order to determine where the fan vents from the bathroom you will need to find a way to trace the ductwork from the fan to it's exit point.  A camera probe can help with this, or if it's a short enough run you might even try a flashlight and a 2nd person looking at the hall vent to see if they see the light.

If the vent is confirmed to be venting inside the house the only way to correct this is to open the walls/ceiling of the bathroom in question and re-run the ductwork.  Something that should be done as the point of the fan is to remove moisture from the bathroom (not smells although that's a secondary benefit) and get it out of the house to reduce mold risk.