You can cut if off or leave it alone, it’s not a major issue, just be careful, don’t’ hurt the healthy part.
I would just leave it alone, because your phal is dehydrated and relative weak. It’s hard to tell which part of stem is still alive, if you hurt the healthy part of stem, the phal will consume energy to heal the wound, that’s not good for the new growth. Just clean the whole plant, and repot the black part of stem into media. The black (or maybe dead) stem can help your phal sit steady in the pot. If you still have the rotting problem, that means you have to examine your watering management & environments. My phal with black stem recovered very well without cutting stem.
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