I wouldn't be cutting nice growing roots off. It is possible they got jarred. But I would observe and see what happens before removing nice looking roots. You could cut off that old black piece below the roots and treat the cut end with some Physan or alcohol. It may be near time to pot this up. I would recommend a clear pot with lots of holes and a mix of sphagnum and medium bark chunks. Remember Phals need to have almost dry media before watering again. It has come a long way and I think it will be fine. Do not over pot it as the media will stay wet for too long.
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