Question #216109 on Yade changed:
https://answers.launchpad.net/yade/+question/216109

    Status: Open => Solved

wangxiaoliang confirmed that the question is solved:
problem is solved thanks to Jakob

people who have the same problem please refer to 
https://answers.launchpad.net/yade/+question/204526

first delete the interactions and then erase the particle 
for i in O.bodies[id].intrs():
  O.interactions.erase(i.id1,i.id2)
O.bodies.erase(id)
O.run(1,True)

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