As I have explained in a previous answer, generally speaking, the law does not prescribe any maximum time period for completion of investigation and filing of charge sheet. Please read that answer for more details.
The answer to your question would be the same. Even if the FIR was registered as per the order of the Supreme Court, the law remains the same with regard to completion of investigation and filing of the charge sheet.
However, at the same time, if the Supreme Court itself has directed the investigating agency to complete the investigation within any specific time period, then the investigating agency will have to comply with such direction. And, if the agency cannot complete the investigation within that specified period, if any, then it may have to seek extension of time period to complete the investigation, from the Supreme Court.
Moreover, I may also point out that even if no such time period has been specified by the Supreme Court for completion of the investigation, usually the investigating agency would be more alert and would give priority to the investigation, if the FIR was directed to be registered by the Supreme Court. If the investigating agency is taking unusually long period of time to complete investigation (depending on the nature and complexity of the case), the person concerned can approach the Supreme Court for expeditious investigation if it was an important case.
Dr. Ashok Dhamija is a New Delhi based Supreme Court Advocate and author of law books. Read more about him by clicking here. List of his Forum Replies. List of his other articles. List of his Quora Answers. List of his YouTube Videos.