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You may try filling on Application for correction in the name of your father, along with reasons for delay. If the authorities do not agree,then you may have to approach the high court by filling a writ petition under Article 226 of the constitution. It is no guarantee that you will get success, but this is what can be tried.it is said that laws helps those who are careful.
Otherwise, if it is really a serious issue for you, you can consider requesting your father to change his name by following the process for the same, which includes the publishing the change of name in the official Gazette of the state government.
By Determination one can Accomplish anything