If you are running a different job, then you would have to reset the program coordinates. If you are running the same file then the part should cut correctly. For 3-D routing operations, my program and machine 0 are never the same. This allows me to move the spindle to a manual tool change position. However, when I use Flashcut for plasma cutting, I prefer to zero the program and machine so I can select an unused protion of metal to cut from.