You should not have taken back the criminal complaint. Anyway what is done is done.
I believe you are more interested in the present and future of your niece than the previous complaint. Now that she is five years old and her father has anyway legally given you proper custody of the child you can easily seek maintenance for her without jeopardising the custody.
But this issue involves a lot of technicalities and all the paper work of custody has to be handled sensitively. In my opinion you better take the authorisation issued by the father to a lawyer and consult in person. You must also seek opportunities to revive the criminal complaint if you can as that will add to your claim of custody of the child instead of the father.
In fact retrieval of the forensic report might aid your attempt of reviving the complaint. But how can you be so sure that the body was sent for forensic investigation? if it was then you need to write a letter to the center for such report, failing which you must send a legal notice and file a criminal complaint against the center pressurising them to publish the report.