I can’t get any clear idea whether you got any permission from D.I/S regarding your B.Ed training. if ot, then immediately put the matter before the concerned D.I/S. Otherwise you may face problem to show your B.Ed degree. Even you are trying to complete this course by taking leave without pay, then also you may be in trouble. Please give the details regarding queries.
No trouble to face in future because he has almost completed the course. As far as I understood from his post, only the exam is due after his joining the post. In such case he is just to apply in Plain paper for permission with the Copy of Exam-Programme to complete the course.