Question about dead stems

[kargren]

So I was growing some plants and a few of them started to die a bit until I moved them from soil growing to hydroponic growing and they are starting to come back into it a bit, but some of the plants have dead portions. Should I cut them off or will this hurt the plant? The plants in question are really just seedlings no more the 4 inches tall 2 inches of which is dead and shriveled brown but the roots and other 2 inches are nice healthy green.