Domestic Enquiry and Legal Proceedings
A domestic enquiry by the firm should have been conducted first, and guilt established. Documents that were manipulated, the amounts involved, how the manipulation took place, the loss to the company, and how much was illegally gained by the concerned employees need to be elucidated and proved. Once this proof is available, they could have dismissed the employees and lodged an FIR as well.
Placing the cart before the horse approach can only complicate legal matters. The police may not do such a skillful job of proving manipulation and misappropriation of company funds. One needs to take actions carefully, keeping all aspects in mind. Avoid hurried steps that will delay the whole proceedings.