How to heal someone who has "neurotic" after practicing meditation on the crown chakra for a long duration (of course due to ignorance)?
We, ourselves, can never heal anyone of anything. It is God’s healing power alone, which can heal a person. However, we can help by being channels for divine healing energy, especially by using Yogananda’s healing prayer techniques and visualizing the person as being whole, well, and surrounded by God’s healing light. Please send your friend’s name to the Ananda Healing Prayer Council, either in the USA or in India. Check out our websites to learn how to do that.
Regarding meditating on the crown chakra for long periods: Yes, I have heard Swami Kriyananda, quoting Paramhansa Yogananda, speak about the harm that this sort of practice can do to a person, especially how it can create neurosis. However, if, as you say, the person was ignorant and did not know that this was not a healthy thing to do, then, of course, it is not entirely his or her fault, unless you take into account, their karmic patterns from the past. Unfortunately, many books and teachers on the chakras suggest meditating on the crown chakra or running energy in and out of it, which are never healthy things to do.
If you have the opportunity to mention gently to this person that it is important never to do this sort of practice again, it might be helpful for him or her to hear. If the neurosis has progressed too far, then it may not work to say this. In any case, always be encouraging and positive with people. With God, all things are possible, including healing neurotic behavior.