If a prosecution document, such as FIR, is lost, it will generally benefit the accused since the burden lies on the prosecution to prove the case.
However, the mere fact that the FIR is missing from the court records does not mean that it cannot be produced from other sources, such as the police station. The original FIR is a “primary evidence”, which if not available, its copy which is a “secondary evidence” of the same document, can be produced by following the procedure laid down in the Evidence Act. It will, of course, be possible for the accused to question the genuineness of such copy.
Moreover, if the FIR has been prepared in the police station in 2-3 copies in the beginning itself by the same uniform process, each such copy may be considered as the “primary evidence” in accordance with the provisions of the Evidence Act.
Please see the relevant provisions of the Evidence Act in this regard.