Matter in the Labour Court, under the Industrial Disputes Act, does not preclude an employer to file an FIR for any crime comitted by an employee/worker in violation of criminal laws. Police necessarly has to make investigation in criminal cases. A Labour Court cannot intervene in such a matter.
If the document is actually a forged document, the worker in his own interest must have refrained from filing a dispute with the Labour Court. Apparently, the employer seemed to have got irritated by the act of the worker in filing a dispute with the Labour Court.
However, if the document is not forged one, the worker should not be afraid of any FIR. If he can satisfy the police about the genuineness of the document that can rather help him to win the case in Labour Court also and that too without extra waste of time.